Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold185
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1073966
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.28
Warning! 182459 characters in sequence are not A, C, G, or T
File 4 of 7
Found at i:300652 original size:20 final size:20
Alignment explanation
Indices: 300627--300682 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
300617 AAAAACCTAG
*
300627 AATGTATCGATACAATGAAT
1 AATGTATCGATACAATCAAT
* *
300647 AATGTATCGATACATTCATT
1 AATGTATCGATACAATCAAT
*
300667 TATGTATCGATACAAT
1 AATGTATCGATACAAT
300683 TTTTTCAGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACAATCAAT
Found at i:300741 original size:20 final size:21
Alignment explanation
Indices: 300713--300764 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
300703 TTCTTGAAAA
* *
300713 GTATCGATATATTCACTTA-T
1 GTATCGATACATTAACTTACT
*
300733 GTATTGATACATTAACTTACT
1 GTATCGATACATTAACTTACT
300754 GTATCGATACA
1 GTATCGATACA
300765 AATTATAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (21 bp):
GTATCGATACATTAACTTACT
Found at i:301256 original size:17 final size:18
Alignment explanation
Indices: 301229--301264 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
301219 TATTTGAATG
301229 TAATAAAAATATAAAAAT
1 TAATAAAAATATAAAAAT
*
301247 TAAT-AAAATATTAAAAT
1 TAATAAAAATATAAAAAT
301264 T
1 T
301265 CAAAGGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TAATAAAAATATAAAAAT
Found at i:303030 original size:15 final size:15
Alignment explanation
Indices: 303011--303049 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
303001 TTATATTTTT
*
303011 TAATTTATTCTTTTAA
1 TAATTTAAT-TTTTAA
303027 -AATTTAATTTTTAA
1 TAATTTAATTTTTAA
303041 TAATTTAAT
1 TAATTTAAT
303050 AATTTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
TAATTTAATTTTTAA
Found at i:309711 original size:30 final size:30
Alignment explanation
Indices: 309675--309736 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
309665 GTTGTCAGAC
309675 TATGATCTTAACTACAAAGGCAAAATCTTT
1 TATGATCTTAACTACAAAGGCAAAATCTTT
309705 TATGATCTTAACTACAAAGGCAAAATCTTT
1 TATGATCTTAACTACAAAGGCAAAATCTTT
309735 TA
1 TA
309737 ACTATTTAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (30 bp):
TATGATCTTAACTACAAAGGCAAAATCTTT
Found at i:311317 original size:42 final size:42
Alignment explanation
Indices: 311257--311339 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
311247 TGTTAAAATA
* *
311257 TTTGTTTTTTACTCTTAAGGAATCAATAACATTTCTTGAATG
1 TTTGTTTTTCACTCTTAAGGAATCAAGAACATTTCTTGAATG
* *
311299 TTTGTTTTTCACTTTTAAGGAATGAAGAACATTTCTTGAAT
1 TTTGTTTTTCACTCTTAAGGAATCAAGAACATTTCTTGAAT
311340 ACAAAGAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (42 bp):
TTTGTTTTTCACTCTTAAGGAATCAAGAACATTTCTTGAATG
Found at i:312778 original size:51 final size:52
Alignment explanation
Indices: 312723--312843 Score: 154
Period size: 51 Copynumber: 2.3 Consensus size: 52
312713 TGAAAAGAAT
* * *
312723 ATGTATCGATACATTTTTCATTATATCGATATATTCT-GGGTTTTGACTTAA
1 ATGTATCGATACATTTTTCATTATATCGATAAATTCTAAGGTTTTGACTCAA
* * * * *
312774 ATGTATTGATACATTATTCGTTGTATCGATAAATTCTAAGTTTTTGACTCAA
1 ATGTATCGATACATTTTTCATTATATCGATAAATTCTAAGGTTTTGACTCAA
*
312826 ATATATCGATACATTTTT
1 ATGTATCGATACATTTTT
312844 TAATGTATCG
Statistics
Matches: 58, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
51 32 0.55
52 26 0.45
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (52 bp):
ATGTATCGATACATTTTTCATTATATCGATAAATTCTAAGGTTTTGACTCAA
Found at i:312851 original size:52 final size:51
Alignment explanation
Indices: 312726--312856 Score: 154
Period size: 52 Copynumber: 2.5 Consensus size: 51
312716 AAAGAATATG
* * * * *
312726 TATCGATACATTTTTCATTATATCGATATATTCTGGGTTTTGACTTAAATG
1 TATCGATACATTTTTCATTGTATCGATAAATTCTAGGTTTTGACTCAAATA
* * * *
312777 TATTGATACATTATTCGTTGTATCGATAAATTCTAAGTTTTTGACTCAAATA
1 TATCGATACATTTTTCATTGTATCGATAAATTCT-AGGTTTTGACTCAAATA
* *
312829 TATCGATACATTTTTTAATGTATCGATA
1 TATCGATACATTTTTCATTGTATCGATA
312857 CATGTAGGCT
Statistics
Matches: 65, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
51 29 0.45
52 36 0.55
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (51 bp):
TATCGATACATTTTTCATTGTATCGATAAATTCTAGGTTTTGACTCAAATA
Found at i:315276 original size:78 final size:77
Alignment explanation
Indices: 315165--315567 Score: 260
Period size: 79 Copynumber: 5.1 Consensus size: 77
315155 TTTACCATTA
* * * * *
315165 AGGATACTCTAATCCCATTATCTCTGAGAGGATACTCCAACCCTGTTTTTATTTTCAAAATATTA
1 AGGATACTCCAA-CCCATTATTTCTAAGGGGATACTCCAACCCTATTTTTA-TTTCAAAATATTA
315230 AAATTTTCATCTC-
64 AAATTTTCATCTCG
* * * *
315243 AGGATACTCCAACCTCATTATTTCTAAGGGGATACTTCAACCTTATTTTTATCTCCAAAATATCA
1 AGGATACTCCAACC-CATTATTTCTAAGGGGATACTCCAACCCTATTTTTAT-TTCAAAATATTA
*
315308 AAATTTTCATCTCA
64 AAATTTTCATCTCG
* * * * * *
315322 ATGATGCTTCAACCCCATCATTTTCGAA-GGGATACTCTAA-CCTCATTTTTATTTCTAAAATAT
1 AGGATACTCCAA-CCCATTA-TTTCTAAGGGGATACTCCAACCCT-ATTTTTATTTC-AAAATAT
*
315385 T-AAATTTTCACCATCG
62 TAAAATTTTCATC-TCG
* * * * * * * * * * * ** *
315401 GGGTTACTCCAACCCCATCATTTTTGAGAGAATACTCTAACCTTGTGTTTACTGCCAAAATA-TC
1 AGGATACTCCAA-CCCATTATTTCTAAGGGGATACTCCAACCCTATTTTTA-TTTCAAAATATTA
* * *
315465 GAATTTTCACCATTG
64 AAATTTTCATC-TCG
* * * * * *
315480 -GAGACACTCCAACCCATTCATTTCCAAAGGGATACTCCAGCCCCATTTTTACTTCAAAAATATT
1 AG-GATACTCCAACCCATT-ATTTCTAAGGGGATACTCCAACCCTATTTTTATTTC-AAAATATT
315544 AAAATTTTCATCTCG
63 AAAATTTTCATCTCG
*
315559 GGGATACTC
1 AGGATACTC
315568 TAACTCTGAT
Statistics
Matches: 247, Mismatches: 61, Indels: 33
0.72 0.18 0.10
Matches are distributed among these distances:
77 3 0.01
78 90 0.36
79 131 0.53
80 23 0.09
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (77 bp):
AGGATACTCCAACCCATTATTTCTAAGGGGATACTCCAACCCTATTTTTATTTCAAAATATTAAA
ATTTTCATCTCG
Found at i:323291 original size:13 final size:13
Alignment explanation
Indices: 323273--323297 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
323263 ATCACTTAAA
323273 TGTATCGATACAT
1 TGTATCGATACAT
323286 TGTATCGATACA
1 TGTATCGATACA
323298 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:323362 original size:52 final size:52
Alignment explanation
Indices: 323306--323434 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
323296 CACTGATCTT
*
323306 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* **
323358 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
323410 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
323435 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:337297 original size:1 final size:1
Alignment explanation
Indices: 337291--337346 Score: 67
Period size: 1 Copynumber: 56.0 Consensus size: 1
337281 CGTCCTCCAC
* * * * *
337291 AAAAAAAAAACAAAAAAAAAAAAAAACAAAACAAAAAAAAACAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
337347 GGGGTCCGGA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:337312 original size:16 final size:16
Alignment explanation
Indices: 337291--337346 Score: 87
Period size: 16 Copynumber: 3.5 Consensus size: 16
337281 CGTCCTCCAC
337291 AAAAAAAAAACAAAAA
1 AAAAAAAAAACAAAAA
337307 AAAAAAAAAAC-AAAA
1 AAAAAAAAAACAAAAA
*
337322 CAAAAAAAAACAAAAA
1 AAAAAAAAAACAAAAA
337338 CAAAAAAAA
1 -AAAAAAAA
337347 GGGGTCCGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
15 14 0.39
16 15 0.42
17 7 0.19
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAACAAAAA
Found at i:338881 original size:35 final size:35
Alignment explanation
Indices: 338806--338916 Score: 118
Period size: 35 Copynumber: 3.2 Consensus size: 35
338796 CTCTGTGGCA
* * * *
338806 CCCTTTTAAAGCCCACAATTTCGCGACGCTC-TTTT
1 CCCTTTT-AAGCCCACAACTTCGTGGCACTCTTTTT
* *
338841 GCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTT
1 CCCTTTTAAGCCCACAACTTCGTGGCACTCTTTTT
* **
338876 CCCTTTTAAGTCCACAACTTCGTGGCA-TCTTTCA
1 CCCTTTTAAGCCCACAACTTCGTGGCACTCTTTTT
338910 CCCTTTT
1 CCCTTTT
338917 TAAAACCCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 30 0.47
35 34 0.53
ACGTcount: A:0.18, C:0.34, G:0.12, T:0.36
Consensus pattern (35 bp):
CCCTTTTAAGCCCACAACTTCGTGGCACTCTTTTT
Found at i:338995 original size:63 final size:65
Alignment explanation
Indices: 338917--339082 Score: 254
Period size: 63 Copynumber: 2.6 Consensus size: 65
338907 TCACCCTTTT
*
338917 TAAAACCCACACAAGTCGGTGGCAACCCTTCCTAAAGCCCACACAAGTTGGTGGCAACC-CCCTC
1 TAAAGCCCACACAAGTCGGTGGCAACCCTTCCTAAAGCCCACACAAGTTGGTGGCAACCACCCTC
**
338981 -AAAGCCCACACAAGTCGGTGGCAACCC-TCTCTAAAGCCCACACAAGTTGGTGGCAACCATTCT
1 TAAAGCCCACACAAGTCGGTGGCAACCCTTC-CTAAAGCCCACACAAGTTGGTGGCAACCACCCT
339044 C
65 C
339045 TAAAGCCCACACAAGTCGGTGGCAA-CCTT-CT-AAGCCCA
1 TAAAGCCCACACAAGTCGGTGGCAACCCTTCCTAAAGCCCA
339083 ATATAGATGG
Statistics
Matches: 95, Mismatches: 3, Indels: 10
0.88 0.03 0.09
Matches are distributed among these distances:
62 9 0.09
63 56 0.59
64 5 0.05
65 25 0.26
ACGTcount: A:0.30, C:0.36, G:0.18, T:0.16
Consensus pattern (65 bp):
TAAAGCCCACACAAGTCGGTGGCAACCCTTCCTAAAGCCCACACAAGTTGGTGGCAACCACCCTC
Found at i:339050 original size:33 final size:32
Alignment explanation
Indices: 338917--339075 Score: 232
Period size: 32 Copynumber: 5.0 Consensus size: 32
338907 TCACCCTTTT
*
338917 TAAAACCCACACAAGTCGGTGGCAACCCTTC-C
1 TAAAGCCCACACAAGTCGGTGGCAA-CCTTCTC
* **
338949 TAAAGCCCACACAAGTTGGTGGCAACCCCCTC
1 TAAAGCCCACACAAGTCGGTGGCAACCTTCTC
*
338981 -AAAGCCCACACAAGTCGGTGGCAACCCTCTC
1 TAAAGCCCACACAAGTCGGTGGCAACCTTCTC
*
339012 TAAAGCCCACACAAGTTGGTGGCAACCATTCTC
1 TAAAGCCCACACAAGTCGGTGGCAACC-TTCTC
339045 TAAAGCCCACACAAGTCGGTGGCAACCTTCT
1 TAAAGCCCACACAAGTCGGTGGCAACCTTCT
339076 AAGCCCAATA
Statistics
Matches: 115, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
31 32 0.28
32 53 0.46
33 30 0.26
ACGTcount: A:0.30, C:0.35, G:0.18, T:0.17
Consensus pattern (32 bp):
TAAAGCCCACACAAGTCGGTGGCAACCTTCTC
Found at i:339889 original size:52 final size:52
Alignment explanation
Indices: 339804--339932 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
339794 CACTGATCTT
*
339804 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATAAAA
* * **
339856 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATAAAA
339908 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
339933 TCATATTTGG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATAAAA
Found at i:345988 original size:28 final size:29
Alignment explanation
Indices: 345956--346017 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
345946 TTGGTCGATC
345956 TATTAAAATTAAAATTTA-ATAATTTA-TA
1 TATTAAAATT-AAATTTATATAATTTATTA
* * *
345984 TATTAATATTATATTTATATATTTTATTA
1 TATTAAAATTAAATTTATATAATTTATTA
346013 TATTA
1 TATTA
346018 TATTATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 6 0.21
28 16 0.55
29 7 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
TATTAAAATTAAATTTATATAATTTATTA
Found at i:346011 original size:5 final size:5
Alignment explanation
Indices: 345982--346024 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
345972 TAATAATTTA
*
345982 TATAT TAATAT TATAT T-TA- TATAT TTTAT TATAT TATAT TATA
1 TATAT T-ATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA
346025 AAATTTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
3 1 0.03
4 4 0.12
5 23 0.70
6 5 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:346030 original size:23 final size:24
Alignment explanation
Indices: 345984--346032 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
345974 ATAATTTATA
*
345984 TATTAATATTATATTTATATATTT
1 TATTAATATTATATTTATAAATTT
346008 TATT-ATATTATA-TTATAAAATTT
1 TATTAATATTATATTTAT-AAATTT
346031 TA
1 TA
346033 AAAAATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 15 0.65
24 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TATTAATATTATATTTATAAATTT
Found at i:346084 original size:29 final size:30
Alignment explanation
Indices: 346048--346172 Score: 98
Period size: 33 Copynumber: 4.1 Consensus size: 30
346038 TTAAATATGA
346048 TTAAATT-TTAAAAAAATAAAAAATTATTT
1 TTAAATTATTAAAAAAATAAAAAATTATTT
*
346077 TTAAATT-TT--AAGAATAAAAAATTATATT
1 TTAAATTATTAAAAAAATAAAAAATTAT-TT
** * *
346105 TTAAAATTATATTTAAAAAT-AATATTTATTT
1 TT-AAATTAT-TAAAAAAATAAAAAATTATTT
* *
346136 TTAATATTATTAAATTAAATAAAATATTTATTT
1 TTAA-ATTATTAAA-AAAATAAAA-AATTATTT
346169 TTAA
1 TTAA
346173 TATAATTTAA
Statistics
Matches: 78, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
27 15 0.19
28 4 0.05
29 14 0.18
30 5 0.06
31 14 0.18
32 9 0.12
33 17 0.22
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (30 bp):
TTAAATTATTAAAAAAATAAAAAATTATTT
Found at i:346100 original size:27 final size:29
Alignment explanation
Indices: 346048--346109 Score: 92
Period size: 27 Copynumber: 2.2 Consensus size: 29
346038 TTAAATATGA
346048 TTAAATTTTAAAAAAATAAAAAATTAT-TT
1 TTAAATTTT-AAAAAATAAAAAATTATATT
*
346077 TTAAATTTT-AAGAATAAAAAATTATATT
1 TTAAATTTTAAAAAATAAAAAATTATATT
346105 TTAAA
1 TTAAA
346110 ATTATATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
27 15 0.48
28 7 0.23
29 9 0.29
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (29 bp):
TTAAATTTTAAAAAATAAAAAATTATATT
Found at i:346110 original size:13 final size:13
Alignment explanation
Indices: 346093--346132 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
346083 TTTAAGAATA
346093 AAAAATTATATTT
1 AAAAATTATATTT
*
346106 TAAAATTATATTT
1 AAAAATTATATTT
*
346119 AAAAATAATATTT
1 AAAAATTATATTT
346132 A
1 A
346133 TTTTTAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AAAAATTATATTT
Found at i:346154 original size:33 final size:33
Alignment explanation
Indices: 346117--346211 Score: 104
Period size: 33 Copynumber: 2.8 Consensus size: 33
346107 AAAATTATAT
*
346117 TTAAA-AATAATATTTATTTTTAATATTATTAAA
1 TTAAATAA-AATATTTATTTTTAATATAATTAAA
*
346150 TTAAATAAAATATTTATTTTTAATATAATTTAAT
1 TTAAATAAAATATTTATTTTTAATATAA-TTAAA
*
346184 TTAAGATAAAAATAATTT-TTATTAATAT
1 TTAA-AT-AAAAT-ATTTATTTTTAATAT
346212 TTTATATTAT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
33 24 0.44
34 10 0.19
35 2 0.04
36 14 0.26
37 4 0.07
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (33 bp):
TTAAATAAAATATTTATTTTTAATATAATTAAA
Found at i:346442 original size:117 final size:114
Alignment explanation
Indices: 346233--346461 Score: 332
Period size: 117 Copynumber: 2.0 Consensus size: 114
346223 TTTAAAATTT
* *
346233 TTTTATTTTTTCGTGGGATAACAAAACTTCTCTTAGATACAAAATTGGTTCTGACTAGCATAGGA
1 TTTTATTTTATCGTGGGATAACAAAACTTCTCTTAGATACAAAATTGGATCTGACTAGCATAGGA
346298 TCCCACATGTCTGCATTCAACTAAAGTAATCTGCATCCTCTTTTGCTGC
66 TCCCACATGTCTGCATTCAACTAAAGTAATCTGCATCCTCTTTTGCTGC
* * * * *
346347 TTTTATTTTATGGTGTGATAACAAAGCTTCTCTTGTGGGATACAACATTGGATCTGACTAGCATA
1 TTTTATTTTATCGTGGGATAACAAAACTTCTC-T-T-AGATACAAAATTGGATCTGACTAGCATA
* * * *
346412 GGATCCCACATTTCTGCATTTAACTGAAGTAATCTTCATCCTCTTTTGCT
63 GGATCCCACATGTCTGCATTCAACTAAAGTAATCTGCATCCTCTTTTGCT
346462 CAGCGTCAAT
Statistics
Matches: 101, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
114 28 0.28
115 1 0.01
116 1 0.01
117 71 0.70
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (114 bp):
TTTTATTTTATCGTGGGATAACAAAACTTCTCTTAGATACAAAATTGGATCTGACTAGCATAGGA
TCCCACATGTCTGCATTCAACTAAAGTAATCTGCATCCTCTTTTGCTGC
Found at i:347580 original size:13 final size:12
Alignment explanation
Indices: 347553--347611 Score: 59
Period size: 13 Copynumber: 4.8 Consensus size: 12
347543 AATATGATCT
*
347553 TATAAATATAAA
1 TATAAATAAAAA
347565 TATAACATAAAAA
1 TATAA-ATAAAAA
347578 TATGAAAT--AAA
1 TAT-AAATAAAAA
347589 TATAACATAAAAA
1 TATAA-ATAAAAA
347602 TATGAAATAA
1 TAT-AAATAA
347612 TATAATAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
10 2 0.05
11 8 0.20
12 5 0.12
13 21 0.52
14 4 0.10
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.27
Consensus pattern (12 bp):
TATAAATAAAAA
Found at i:347590 original size:24 final size:24
Alignment explanation
Indices: 347560--347616 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
347550 TCTTATAAAT
347560 ATAAATATAACATAAAAATATGAA
1 ATAAATATAACATAAAAATATGAA
347584 ATAAATATAACATAAAAATATGAA
1 ATAAATATAACATAAAAATATGAA
347608 AT-AATATAA
1 ATAAATATAA
347617 TAAATATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 7 0.21
24 26 0.79
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.26
Consensus pattern (24 bp):
ATAAATATAACATAAAAATATGAA
Found at i:347642 original size:38 final size:35
Alignment explanation
Indices: 347599--347692 Score: 88
Period size: 32 Copynumber: 2.6 Consensus size: 35
347589 TATAACATAA
* *
347599 AAATATGAAATAATATAATAAATATTTTAAAATTTTTAT
1 AAATAT-AAATAATAT--T-AATATATTAAAATTTATAT
347638 -AATATAAAT--TATTAATATATTAAAATTTATAT
1 AAATATAAATAATATTAATATATTAAAATTTATAT
347670 AAATATAAAATAAT-TTAAATATA
1 AAATAT-AAATAATATT-AATATA
347693 ATTATAATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
32 17 0.35
33 6 0.12
34 4 0.08
35 5 0.10
36 7 0.15
37 4 0.08
38 5 0.10
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (35 bp):
AAATATAAATAATATTAATATATTAAAATTTATAT
Found at i:347676 original size:20 final size:19
Alignment explanation
Indices: 347651--347716 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 19
347641 ATAAATTATT
347651 AATATATTAAAATTTATATA
1 AATATA-TAAAATTTATATA
*
347671 AATATAAAATAATTTAAATATA
1 AATATATAA-AATTT--ATATA
*
347693 ATTATAATAAAA--TATATA
1 AATAT-ATAAAATTTATATA
347711 AATATA
1 AATATA
347717 ATATAAATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.24
19 2 0.05
20 12 0.32
22 11 0.29
23 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATATATAAAATTTATATA
Found at i:347711 original size:18 final size:19
Alignment explanation
Indices: 347688--347735 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 19
347678 AATAATTTAA
347688 ATATAATTATAATA-AAAT
1 ATATAATTATAATATAAAT
*
347706 ATATAAATATAATATAAAT
1 ATATAATTATAATATAAAT
347725 ATATGAATTAT
1 ATAT-AATTAT
347736 CAAATTCGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 13 0.50
19 8 0.31
20 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
ATATAATTATAATATAAAT
Found at i:347712 original size:24 final size:24
Alignment explanation
Indices: 347666--347722 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
347656 ATTAAAATTT
*
347666 ATATAA-AT-ATAAAATAATTTAA
1 ATATAATATAATAAAATAATATAA
347688 ATATAATTATAATAAAAT-ATATAA
1 ATATAA-TATAATAAAATAATATAA
347712 ATATAATATAA
1 ATATAATATAA
347723 ATATATGAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 6 0.19
23 5 0.16
24 13 0.42
25 7 0.23
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
ATATAATATAATAAAATAATATAA
Found at i:347724 original size:11 final size:11
Alignment explanation
Indices: 347635--347727 Score: 59
Period size: 11 Copynumber: 8.4 Consensus size: 11
347625 TTAAAATTTT
347635 TATAATATAAA
1 TATAATATAAA
*
347646 TTATTAATAT-AT
1 -TA-TAATATAAA
* * *
347658 TAAAATTTATA
1 TATAATATAAA
347669 TA-AATATAAA
1 TATAATATAAA
*
347679 -ATAATTTAAA
1 TATAATATAAA
347689 TATAAT-TATAA
1 TATAATATA-AA
*
347700 TAAAATATATAAA
1 T-ATA-ATATAAA
347713 TATAATATAAA
1 TATAATATAAA
347724 TATA
1 TATA
347728 TGAATTATCA
Statistics
Matches: 63, Mismatches: 10, Indels: 17
0.70 0.11 0.19
Matches are distributed among these distances:
9 1 0.02
10 19 0.30
11 23 0.37
12 7 0.11
13 11 0.17
14 2 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TATAATATAAA
Found at i:347734 original size:38 final size:38
Alignment explanation
Indices: 347635--347735 Score: 100
Period size: 40 Copynumber: 2.6 Consensus size: 38
347625 TTAAAATTTT
*
347635 TATAATATAAAT-TATTAA-TATATTAAAATTTATATAAA
1 TATAATATAAATATA-TAATTATAATAAAA-TTATATAAA
* *
347673 TATAAAATAATTTAAATATAATTATAATAAAA-TATATAAA
1 TATAATATAA---ATATATAATTATAATAAAATTATATAAA
347713 TATAATATAAATATATGAATTAT
1 TATAATATAAATATAT-AATTAT
347736 CAAATTCGAT
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
37 5 0.10
38 15 0.29
40 17 0.33
41 4 0.08
42 11 0.21
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (38 bp):
TATAATATAAATATATAATTATAATAAAATTATATAAA
Found at i:348510 original size:21 final size:21
Alignment explanation
Indices: 348485--348525 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
348475 TTTTAAAAAA
*
348485 TTATTTTATAATAATATTTAT
1 TTATTTTATAATAAAATTTAT
348506 TTATTTTATAATAAAATTTA
1 TTATTTTATAATAAAATTTA
348526 AATAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTTTATAATAAAATTTAT
Found at i:350199 original size:24 final size:24
Alignment explanation
Indices: 350171--350231 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
350161 AAAATTTAAA
*
350171 AAATAATTTTTTAATTAA-ATTTTT
1 AAAT-ATTTTTTAATTAATACTTTT
*
350195 TAATATTATTTTAATTAATACTTTT
1 AAATATT-TTTTAATTAATACTTTT
350220 AAATATTTTTTA
1 AAATATTTTTTA
350232 TATATATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 3 0.09
24 18 0.56
25 11 0.34
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
AAATATTTTTTAATTAATACTTTT
Found at i:351215 original size:17 final size:16
Alignment explanation
Indices: 351172--351214 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
351162 TTGAGTGTAT
*
351172 TTTTAAATATGAATATA
1 TTTT-AATATAAATATA
351189 TATTTAATATAAATATA
1 T-TTTAATATAAATATA
351206 TTTT-ATATA
1 TTTTAATATA
351215 TTTACACAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 5 0.21
16 3 0.12
17 13 0.54
18 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
TTTTAATATAAATATA
Found at i:352399 original size:14 final size:14
Alignment explanation
Indices: 352376--352407 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
352366 AAATTTTAGT
352376 AATT-TAAAAATAA
1 AATTATAAAAATAA
352389 AATTATAAAAATAA
1 AATTATAAAAATAA
352403 AATTA
1 AATTA
352408 CATCAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AATTATAAAAATAA
Found at i:356325 original size:15 final size:15
Alignment explanation
Indices: 356307--356335 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
356297 TCACTTCATC
356307 ACTTGAGTTTTCACA
1 ACTTGAGTTTTCACA
356322 ACTTGAGTTTTCAC
1 ACTTGAGTTTTCAC
356336 TGTTGGTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (15 bp):
ACTTGAGTTTTCACA
Found at i:356786 original size:2 final size:2
Alignment explanation
Indices: 356779--356811 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
356769 TCATAACCGA
356779 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
356812 AAAGAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:356897 original size:29 final size:27
Alignment explanation
Indices: 356858--356912 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 27
356848 AATAGTTTTA
* *
356858 AATATTTATATAATTTTATTTATATATTG
1 AATATTAATAT-ATTATATTTA-ATATTG
356887 AATATTAATATATTATATTTAATATT
1 AATATTAATATATTATATTTAATATT
356913 ATCTATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.21
28 9 0.38
29 10 0.42
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
AATATTAATATATTATATTTAATATTG
Found at i:356910 original size:14 final size:13
Alignment explanation
Indices: 356859--356914 Score: 60
Period size: 15 Copynumber: 4.2 Consensus size: 13
356849 ATAGTTTTAA
356859 ATATTTATATAATT
1 ATATTTATAT-ATT
*
356873 TTATTTATATATT
1 ATATTTATATATT
*
356886 GAATATTAATATATT
1 --ATATTTATATATT
356901 ATATTTA-ATATT
1 ATATTTATATATT
356913 AT
1 AT
356915 CTATAATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 7 0.19
13 9 0.25
14 9 0.25
15 11 0.31
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (13 bp):
ATATTTATATATT
Found at i:357623 original size:18 final size:19
Alignment explanation
Indices: 357592--357628 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
357582 TTATTAAAAA
357592 ATATTAATAATTAT-TATT
1 ATATTAATAATTATATATT
357610 ATATTAA-AATTTATATATT
1 ATATTAATAA-TTATATATT
357629 TTGTAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 2 0.12
18 11 0.65
19 4 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATTAATAATTATATATT
Found at i:359303 original size:20 final size:20
Alignment explanation
Indices: 359270--359323 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
359260 TTGATGGCAA
359270 AAATAAAAAA-TCAAAGATC
1 AAATAAAAAAGTCAAAGATC
*
359289 AAATAAAAAAGTC-AAGCTC
1 AAATAAAAAAGTCAAAGATC
359308 AAACT-AAAAAGTCAAA
1 AAA-TAAAAAAGTCAAA
359324 AGTCAAACCA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 26 0.84
20 5 0.16
ACGTcount: A:0.65, C:0.13, G:0.07, T:0.15
Consensus pattern (20 bp):
AAATAAAAAAGTCAAAGATC
Found at i:360743 original size:16 final size:16
Alignment explanation
Indices: 360713--360750 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
360703 ACTTAATTAT
*
360713 AATTA-TTAAATTTGA
1 AATTATTTAAAATTGA
360728 AATTATTTAAAATTGA
1 AATTATTTAAAATTGA
*
360744 TATTATT
1 AATTATT
360751 ATTCTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (16 bp):
AATTATTTAAAATTGA
Found at i:365178 original size:19 final size:19
Alignment explanation
Indices: 365154--365290 Score: 120
Period size: 19 Copynumber: 7.7 Consensus size: 19
365144 AGTGATATAT
365154 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
365173 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
365186 TGTATCGATA-AAACACTTA
1 TGTATCGATACAAA-ACTTA
365205 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
365218 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
*
365237 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
* *
365256 TGTATCGATACAATTACTGTT
1 TGTATCGATACAA-AACT-TA
365277 TGTATCGATACAAA
1 TGTATCGATACAAA
365291 TTGTTGAAAT
Statistics
Matches: 99, Mismatches: 3, Indels: 31
0.74 0.02 0.23
Matches are distributed among these distances:
13 21 0.21
14 2 0.02
16 4 0.04
18 2 0.02
19 53 0.54
20 3 0.03
21 14 0.14
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:365191 original size:13 final size:13
Alignment explanation
Indices: 365173--365229 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
365163 ACAAAACTTA
365173 TGTATCGATACAT
1 TGTATCGATACAT
365186 TGTATCGATAAAACACTT
1 TGTATCGAT---ACA--T
365204 ATGTATCGATACAT
1 -TGTATCGATACAT
365218 TGTATCGATACA
1 TGTATCGATACA
365230 ACACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:365193 original size:32 final size:32
Alignment explanation
Indices: 365147--365248 Score: 170
Period size: 32 Copynumber: 3.2 Consensus size: 32
365137 GCTTCGTAGT
*
365147 GATATATTGTATCGATACAAAACTTATGTATC
1 GATACATTGTATCGATACAAAACTTATGTATC
365179 GATACATTGTATCGATA-AAACACTTATGTATC
1 GATACATTGTATCGATACAAA-ACTTATGTATC
*
365211 GATACATTGTATCGATACAACACTTATGTATC
1 GATACATTGTATCGATACAAAACTTATGTATC
365243 GATACA
1 GATACA
365249 ACACTTATGT
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
31 3 0.05
32 61 0.92
33 2 0.03
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (32 bp):
GATACATTGTATCGATACAAAACTTATGTATC
Found at i:365791 original size:20 final size:20
Alignment explanation
Indices: 365766--365836 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
365756 TACCCTGATG
*
365766 TATCGATACATTTTTCAATA
1 TATCGATACATTTATCAATA
* * *
365786 TATCGATACATGTATGAATG
1 TATCGATACATTTATCAATA
* *
365806 TATCGATACATTGAAT-AATG
1 TATCGATACATT-TATCAATA
365826 TATCGATACAT
1 TATCGATACAT
365837 CTAGTTAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.38
Consensus pattern (20 bp):
TATCGATACATTTATCAATA
Found at i:379758 original size:10 final size:10
Alignment explanation
Indices: 379743--379804 Score: 63
Period size: 10 Copynumber: 5.8 Consensus size: 10
379733 CCTTTACACC
379743 CAAAAAAAAA
1 CAAAAAAAAA
379753 CAAAAAAAAA
1 CAAAAAAAAA
379763 CAAAACAAAAAAA
1 C--AA-AAAAAAA
379776 CAAAAAAAAA
1 CAAAAAAAAA
*
379786 -AGAAAAAATAG
1 CA-AAAAAA-AA
379797 CAAAAAAA
1 CAAAAAAA
379805 TAGAAGGGTC
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
9 1 0.02
10 24 0.53
11 9 0.20
12 3 0.07
13 8 0.18
ACGTcount: A:0.85, C:0.10, G:0.03, T:0.02
Consensus pattern (10 bp):
CAAAAAAAAA
Found at i:379804 original size:1 final size:1
Alignment explanation
Indices: 379744--379793 Score: 55
Period size: 1 Copynumber: 50.0 Consensus size: 1
379734 CTTTACACCC
* * * * *
379744 AAAAAAAAACAAAAAAAAACAAAACAAAAAAACAAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
379794 TAGCAAAAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.90, C:0.08, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:381066 original size:29 final size:29
Alignment explanation
Indices: 381024--381947 Score: 1241
Period size: 28 Copynumber: 32.0 Consensus size: 29
381014 AATGTTCATC
381024 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
381053 CCTTTCAAAGCCCACAAATCAGTGACACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
381082 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
381110 CCTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
381138 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
381167 CTTTTCAAAGCCCACAAGTGAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
381195 CCTTTCAAAACCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
381224 CCTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
381252 CCTTTCAAAGCCCACAAGTTAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
381281 CCTTTCAAAGCCCACAAGTTAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
381310 CCTTTCAAAGCCCACAAATCAGCGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
381339 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
381367 CCTTTCAAAGCCCACAAGTCAGTGGCAAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
381396 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
381425 CTTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
**
381454 TTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
381482 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
381511 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
381540 CTTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
381568 CCTTTCAGAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
381596 CCTTTCGAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
381624 CCTTGCGAAGCCCATAATTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
381653 -CTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
381680 CCTTTTAAAGCCCACACAAGTCAGTGGCACT
1 CCTTTCAAAG-CC-CACAAGTCAGTGGCACT
* * *
381711 CCTTTTAAAGCCTACGCAAGTCAGTGGTAC-
1 CCTTTCAAAGCC--CACAAGTCAGTGGCACT
* *
381741 CTTTTCAAAGCCCACGAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
381770 -CTTTCAAAGCCCACAAGTCAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
381797 CCTTTCAAAGCCCACAAGTCAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
381825 CCTTTCAAAGCCCACGCAAGTCAATGGCAC-
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCACT
* ** *
381855 CCTTTTAAAGCCCACGCAAGTCAGTAACGCT
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCACT
* * *
381886 CTTTTCAAAGCCCACATGTGTCAGTGACAACT
1 CCTTTCAAAGCCCACA--AGTCAGTGGC-ACT
** *
381918 TTTTTCAAAGCCTACACAAGTTAGTGGCAC
1 CCTTTCAAAGCC--CACAAGTCAGTGGCAC
381948 ATTTTTTTTA
Statistics
Matches: 806, Mismatches: 67, Indels: 42
0.88 0.07 0.05
Matches are distributed among these distances:
27 1 0.00
28 345 0.43
29 324 0.40
30 65 0.08
31 47 0.06
32 20 0.02
34 4 0.00
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.22
Consensus pattern (29 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:381285 original size:86 final size:87
Alignment explanation
Indices: 381024--381947 Score: 1241
Period size: 86 Copynumber: 10.7 Consensus size: 87
381014 AATGTTCATC
* * *
381024 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGACACTCTTTTCA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCA
381089 AAGCCCACAAGTCAGTGGCAC-
66 AAGCCCACAAGTCAGTGGCACT
*
381110 CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCA
*
381174 AAGCCCACAAGTGAGTGGCAC-
66 AAGCCCACAAGTCAGTGGCACT
* *
381195 CCTTTCAAAACCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCAC-CCTTTCA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCA
*
381259 AAGCCCACAAGTTAGTGGCACT
66 AAGCCCACAAGTCAGTGGCACT
* * * *
381281 CCTTTCAAAGCCCACAAGTTAGTGGCACTCCTTTCAAAGCCCACAAATCAGCGGCACTCTTTTCA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCA
381346 AAGCCCACAAGTCAGTGGCAC-
66 AAGCCCACAAGTCAGTGGCACT
* *
381367 CCTTTCAAAGCCCACAAGTCAGTGGCAATCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCA
*
381432 AAGCCCACAAATCAGTGGCACT
66 AAGCCCACAAGTCAGTGGCACT
**
381454 TTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCA
381518 AAGCCCACAAGTCAGTGGCACT
66 AAGCCCACAAGTCAGTGGCACT
* * * *
381540 CTTTTCAAAGCCCACAAGTTAGTGGCAC-CCTTTCAGAGCCCACAAGTCAGTGGCAC-CCTTTCG
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCA
381603 AAGCCCACAAGTCAGTGGCAC-
66 AAGCCCACAAGTCAGTGGCACT
* * * * *
381624 CCTTGCGAAGCCCATAATTCAGTGGCACT-CTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTTA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCA
381687 AAGCCCACACAAGTCAGTGGCACT
66 AAG-CC-CACAAGTCAGTGGCACT
* * * * *
381711 CCTTTTAAAGCCTACGCAAGTCAGTGGTAC-CTTTTCAAAGCCCACGAGTCAGTGGCACT-CTTT
1 CCTTTCAAAGCC--CACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTT
381774 CAAAGCCCACAAGTCAGTGGCA-T
64 CAAAGCCCACAAGTCAGTGGCACT
*
381797 CCTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACGCAAGTCAATGGCAC-CCTTT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCA--CAAGTCAGTGGCACTCCTTT
* ** *
381860 TAAAGCCCACGCAAGTCAGTAACGCT
64 CAAAGCCCA--CAAGTCAGTGGCACT
* * * ** *
381886 CTTTTCAAAGCCCACATGTGTCAGTGACAACTTTTTTCAAAGCCTACACAAGTTAGTGGCAC
1 CCTTTCAAAGCCCACA--AGTCAGTGGC-ACTCCTTTCAAAGCC--CACAAGTCAGTGGCAC
381948 ATTTTTTTTA
Statistics
Matches: 749, Mismatches: 64, Indels: 43
0.88 0.07 0.05
Matches are distributed among these distances:
84 82 0.11
85 136 0.18
86 349 0.47
87 75 0.10
88 12 0.02
89 61 0.08
91 8 0.01
92 1 0.00
93 23 0.03
95 2 0.00
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.22
Consensus pattern (87 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCA
AAGCCCACAAGTCAGTGGCACT
Found at i:382540 original size:20 final size:19
Alignment explanation
Indices: 382512--382586 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 19
382502 TTTTACCCTG
*
382512 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTAT-A
* *
382532 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTAT-A
* *
382552 ATGTATCGATATATTCTGTA
1 ATGTATCGATACATT-TATA
382572 ATGTATCGATACATT
1 ATGTATCGATACATT
382587 ATGTCTTTTT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.41
Consensus pattern (19 bp):
ATGTATCGATACATTTATA
Found at i:382579 original size:40 final size:39
Alignment explanation
Indices: 382512--382589 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 39
382502 TTTTACCCTG
*
382512 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTTGTCAATATATCGATACAT-TATGA
* *
382552 ATGTATCGATATATTCTGT-AATGTATCGATACATTATG
1 ATGTATCGATACATT-TGTCAATATATCGATACATTATG
382590 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 4 0.12
40 28 0.82
41 2 0.06
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTTGTCAATATATCGATACATTATGA
Found at i:387240 original size:26 final size:25
Alignment explanation
Indices: 387211--387260 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
387201 TTTTTTGTTT
*
387211 TTAAAAA-TATTTATTTATTTTTTAAA
1 TTAAAAATTA-TTATTT-TTTATTAAA
387237 TTAAAAATTATTATTTTTTATTAA
1 TTAAAAATTATTATTTTTTATTAA
387261 TATACTTGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 13 0.59
27 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TTAAAAATTATTATTTTTTATTAAA
Found at i:388875 original size:139 final size:139
Alignment explanation
Indices: 388721--388999 Score: 522
Period size: 139 Copynumber: 2.0 Consensus size: 139
388711 ACAAACCTAG
388721 GAGAACTTAAAAATTATGGCTAGGATAATATGCTTGTGCATTGTTTTTTAAGAAGATTTAGCATT
1 GAGAACTTAAAAATTATGGCTAGGATAATATGCTTGTGCATTGTTTTTTAAGAAGATTTAGCATT
*
388786 CAAAGAAAAGCATTTTGATGTCTCCTCTATTGTTAAATTGTGTCTTAAAAATGAGTTGAAACATG
66 CAAAGAAAAGCATTTTGATGTCTCCTCTATTGTTAAATTGTGTCTTAAAAATGAGTTGAAACACG
388851 GTCTTTGGA
131 GTCTTTGGA
* *
388860 GAGAACTTAAAAATTATGGCTAGGATAGTATGCTTGTGCATTGTTTTTTAGGAAGATTTAGCATT
1 GAGAACTTAAAAATTATGGCTAGGATAATATGCTTGTGCATTGTTTTTTAAGAAGATTTAGCATT
*
388925 CAAAGGAAAGCATTTTGATGTCTCCTCTATTGTTAAATTGTGTCTTAAAAATGAGTTGAAACACG
66 CAAAGAAAAGCATTTTGATGTCTCCTCTATTGTTAAATTGTGTCTTAAAAATGAGTTGAAACACG
388990 GTCTTTGGA
131 GTCTTTGGA
388999 G
1 G
389000 GTAGAGCATT
Statistics
Matches: 136, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
139 136 1.00
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.37
Consensus pattern (139 bp):
GAGAACTTAAAAATTATGGCTAGGATAATATGCTTGTGCATTGTTTTTTAAGAAGATTTAGCATT
CAAAGAAAAGCATTTTGATGTCTCCTCTATTGTTAAATTGTGTCTTAAAAATGAGTTGAAACACG
GTCTTTGGA
Found at i:391202 original size:270 final size:270
Alignment explanation
Indices: 390721--391227 Score: 879
Period size: 270 Copynumber: 1.9 Consensus size: 270
390711 GACTACTCGC
**
390721 TAAGTTTCGACTAATGCCTTGCCTCCCAATGAAGAAATGATTAATAAAACCAAGTAAGAAAATGA
1 TAAGTTTCGACTAATGCCTTGCCTCCCAATGAAGAAATGAAAAATAAAACCAAGTAAGAAAATGA
390786 AAATCAAGATAAACGGTGATTTTACTTAGTGATTGACAAAAGAAAATTGAAATTTTTATTATAGC
66 AAATCAAGATAAACGGTGATTTTACTTAGTGATTGACAAAAGAAAATTGAAATTTTTATTATAGC
* *
390851 ACGTATAATTTACTTTTATTTATTATTTTATTTTATAAATTTTTCTTTTAGAGATTTCGCATATT
131 ACATATAATTTACTTTTATTTATTATTTTATTTTATAAATTTTCCTTTTAGAGATTTCGCATATT
* *
390916 TAATTAAATTTTTCTCAAAAAGTGTCATTTCGTACCATGATGCCTTGCCTCCTAATGAAGAAATG
196 TAATTAAATTTTTCTCAAAAAATATCATTTCGTACCATGATGCCTTGCCTCCTAATGAAGAAATG
390981 ATTTATTTTA
261 ATTTATTTTA
* ** * *
390991 TAAGTTTCGACTTATGCCTTGCCTCTTAATGAAGAAATGAAAAATAAAACCGAGTAAGCAAATGA
1 TAAGTTTCGACTAATGCCTTGCCTCCCAATGAAGAAATGAAAAATAAAACCAAGTAAGAAAATGA
*
391056 AAATCAAGATAAACGGTGATTTTACTTAGTGATTGACAAAAGAAAATTTAAATTTTTATTATAGC
66 AAATCAAGATAAACGGTGATTTTACTTAGTGATTGACAAAAGAAAATTGAAATTTTTATTATAGC
* *
391121 ACATATAATTTGCTTTTATTTGTTATTTTATTTTATAAATTTTCCTTTTAGAGATTTCGCATATT
131 ACATATAATTTACTTTTATTTATTATTTTATTTTATAAATTTTCCTTTTAGAGATTTCGCATATT
*
391186 TAATTAAATTTTTCTCAAAAAATATCATTTCGTACCTTGATG
196 TAATTAAATTTTTCTCAAAAAATATCATTTCGTACCATGATG
391228 GAAACTCGCC
Statistics
Matches: 222, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
270 222 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (270 bp):
TAAGTTTCGACTAATGCCTTGCCTCCCAATGAAGAAATGAAAAATAAAACCAAGTAAGAAAATGA
AAATCAAGATAAACGGTGATTTTACTTAGTGATTGACAAAAGAAAATTGAAATTTTTATTATAGC
ACATATAATTTACTTTTATTTATTATTTTATTTTATAAATTTTCCTTTTAGAGATTTCGCATATT
TAATTAAATTTTTCTCAAAAAATATCATTTCGTACCATGATGCCTTGCCTCCTAATGAAGAAATG
ATTTATTTTA
Found at i:391420 original size:128 final size:127
Alignment explanation
Indices: 391202--391578 Score: 424
Period size: 128 Copynumber: 2.9 Consensus size: 127
391192 AATTTTTCTC
* * ** **
391202 AAAAAATATCATTTCGTACCTTGATGGAAACTCGCCAAGATAT-AAAAAATTT-GAAATCTTTTA
1 AAAAAA-ATCATTTCGTACCTTAAT-GAAAATCGAAAAGATATGAAAAGTTTTCGAAATCTTTT-
*
391265 ATACCCCTATAGAT-ACCTATAGGAATATAAAAGATTTAAAATGATTAATATTTATTTAT-ATTT
63 ATACCCCTATGGATAACC-ATAGGAATATAAAAGATTTAAAATGATTAATATTTATTTATGATTT
391328 G
127 G
*
391329 AAAAAAATCATTTCATACCTTAATGAAAAATCGAAAAGATATGAAAAGTTTTTCGAAATCTTTTA
1 AAAAAAATCATTTCGTACCTTAATG-AAAATCGAAAAGATATGAAAAG-TTTTCGAAATCTTTTA
* * *
391394 TACCCCTACGGATAACCATAGGAATATAAATA-ACTTAAACATGATTAATATTTATTTATGTTTT
64 TACCCCTATGGATAACCATAGGAATATAAA-AGATTTAAA-ATGATTAATATTTATTTATGATTT
391458 G
127 G
** * * *
391459 AAAAAAATCATTTCGTACCTTAATG-GTATCCAAAAAGATACGAAACGTTTTCGAAATCTTTTAT
1 AAAAAAATCATTTCGTACCTTAATGAAAAT-CGAAAAGATATGAAAAGTTTTCGAAATCTTTTAT
* * * * * * *
391523 ATCCCTATGGATACCCATAGGAACATAAAAGATTAAAAACGATTAACATTTGTTTA
65 ACCCCTATGGATAACCATAGGAATATAAAAGATTTAAAATGATTAATATTTATTTA
391579 AATTAACGAG
Statistics
Matches: 214, Mismatches: 26, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
125 1 0.00
126 29 0.14
127 26 0.12
128 83 0.39
129 47 0.22
130 28 0.13
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (127 bp):
AAAAAAATCATTTCGTACCTTAATGAAAATCGAAAAGATATGAAAAGTTTTCGAAATCTTTTATA
CCCCTATGGATAACCATAGGAATATAAAAGATTTAAAATGATTAATATTTATTTATGATTTG
Found at i:391726 original size:15 final size:16
Alignment explanation
Indices: 391706--391739 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
391696 TACCTATTGG
391706 AAAATAAAAGAT-TTA
1 AAAATAAAAGATGTTA
*
391721 AAAATAATAGATGTTA
1 AAAATAAAAGATGTTA
391737 AAA
1 AAA
391740 TATATTTACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (16 bp):
AAAATAAAAGATGTTA
Found at i:392521 original size:22 final size:23
Alignment explanation
Indices: 392484--392536 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
392474 GTTTTTTTAC
*
392484 CTATTTTCTCTATTTTTCTCTTT
1 CTATTTTCTCTATTTTTCTCTCT
* * *
392507 CTCTTTTCT-TTTTTTTTTCTCT
1 CTATTTTCTCTATTTTTCTCTCT
392529 CTATTTTC
1 CTATTTTC
392537 AGCTGAACAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.72
Consensus pattern (23 bp):
CTATTTTCTCTATTTTTCTCTCT
Found at i:392811 original size:20 final size:20
Alignment explanation
Indices: 392786--392831 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
392776 GAAATTGAAT
*
392786 GGCAACCAAGCTAGTTTCCA
1 GGCAACCAAGCTAGTTGCCA
392806 GGCAACCAAGCTAGTTGCCA
1 GGCAACCAAGCTAGTTGCCA
*
392826 TGCAAC
1 GGCAAC
392832 TAGTTGGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.17
Consensus pattern (20 bp):
GGCAACCAAGCTAGTTGCCA
Found at i:393596 original size:165 final size:168
Alignment explanation
Indices: 393164--393596 Score: 553
Period size: 169 Copynumber: 2.6 Consensus size: 168
393154 ATTTTAGAAA
*
393164 AAAAAAAGAGTTTCAAGG-AAAAAATCAAAAACTCATGAAAATGGATGAATTTTTTAAACTGAAT
1 AAAAACAGAGTTTCAAGGAAAAAAATCAAAAACTCATGAAAATGGATGAATTTTTTAAACTGAAT
* *
393228 TAATATGATATAAATAATGGTATTTGATG-AATTTTAAAAATTAAAAAACCAAGAAAACCCTCCC
66 TAATATGATATAAATATTGGTATTTGA-GAAATTTTAAAAATTAAAAAACCAAGAAAAACCTCCC
* *
393292 TCCGAAAAAAATCACGGAGTAAAATACACTGTATTTCAG
130 TCCGAAAAAAATCAAGGAGTAAAATACACTGTATTGCAG
* * * *
393331 AAAAATAGGAGTTTCAAGGAAAAAATTCAAAAATTTATGAAAATGGATGAATTTTTTAAACTGAA
1 AAAAACA-GAGTTTCAAGGAAAAAAATCAAAAACTCATGAAAATGGATGAATTTTTTAAACTGAA
* *
393396 TTAATATGATATAAATATTGGTATTTGATAAATTTTAAAAATT-AAAAACCAAGAAAAATC-CCC
65 TTAATATGATATAAATATTGGTATTTGAGAAATTTTAAAAATTAAAAAACCAAGAAAAACCTCCC
*
393459 T-CGAAAAAAATTGCAAAGTAG-AAAATA-AC-GTATTGCGAG
130 TCCGAAAAAAA-T-C-AAGGAGTAAAATACACTGTATTGC-AG
* * *
393498 AAAAACA-A-TTTCAAGGAAAAAAATCAAAAACCCATGAAAATGAATTAATTTTTTAAAACTGAA
1 AAAAACAGAGTTTCAAGGAAAAAAATCAAAAACTCATGAAAATGGATGAATTTTTT-AAACTGAA
* * * **
393561 TTAGTGTGAAATAAATATTAATATTTGAGAAATTTT
65 TTAATATGATATAAATATTGGTATTTGAGAAATTTT
393597 GATGTATAAA
Statistics
Matches: 234, Mismatches: 24, Indels: 18
0.85 0.09 0.07
Matches are distributed among these distances:
164 40 0.17
165 39 0.17
166 15 0.06
167 21 0.09
168 33 0.14
169 86 0.37
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.28
Consensus pattern (168 bp):
AAAAACAGAGTTTCAAGGAAAAAAATCAAAAACTCATGAAAATGGATGAATTTTTTAAACTGAAT
TAATATGATATAAATATTGGTATTTGAGAAATTTTAAAAATTAAAAAACCAAGAAAAACCTCCCT
CCGAAAAAAATCAAGGAGTAAAATACACTGTATTGCAG
Found at i:401947 original size:2 final size:2
Alignment explanation
Indices: 401934--401973 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
401924 ATTTAATAAA
* * *
401934 AT AT AA AT AT AT AT GT TT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
401974 CAGTAAACTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:405891 original size:17 final size:17
Alignment explanation
Indices: 405861--405896 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
405851 TTATAATATC
*
405861 CAAGATAACAAAAAATA
1 CAAGACAACAAAAAATA
*
405878 CAAGACAACCAAAAATA
1 CAAGACAACAAAAAATA
405895 CA
1 CA
405897 TCAATGATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.67, C:0.19, G:0.06, T:0.08
Consensus pattern (17 bp):
CAAGACAACAAAAAATA
Found at i:407204 original size:2 final size:2
Alignment explanation
Indices: 407192--407226 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
407182 TTAACCATTT
* *
407192 TA TA GA TA TA TA TA TA TA TA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
407227 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:407231 original size:2 final size:2
Alignment explanation
Indices: 407226--407258 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
407216 TATACATATA
407226 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
407259 CTGAGAAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:409091 original size:22 final size:24
Alignment explanation
Indices: 409065--409116 Score: 83
Period size: 21 Copynumber: 2.3 Consensus size: 24
409055 CAAAATTTTG
409065 AATAAAATATAAATA-ATTT-AAA
1 AATAAAATATAAATATATTTAAAA
409087 AAT-AAATATAAATATATTTAAAA
1 AATAAAATATAAATATATTTAAAA
409110 AATAAAA
1 AATAAAA
409117 AATATAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 11 0.41
22 7 0.26
23 6 0.22
24 3 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (24 bp):
AATAAAATATAAATATATTTAAAA
Found at i:411306 original size:35 final size:38
Alignment explanation
Indices: 411227--411309 Score: 93
Period size: 35 Copynumber: 2.3 Consensus size: 38
411217 AATAATATTA
* * *
411227 AAAAATTAAAAAATTATTTTTATATTAATATTTCTAAT
1 AAAATTTAAAAAAATATTTTTATATTAATATTTCAAAT
*
411265 TAAATTTAAAAAAATA-TTTT-T-TTAATATTT-AAAT
1 AAAATTTAAAAAAATATTTTTATATTAATATTTCAAAT
411299 AATAATTTAAA
1 AA-AATTTAAA
411310 TTAAATCAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
34 4 0.10
35 17 0.44
36 1 0.03
37 4 0.10
38 13 0.33
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (38 bp):
AAAATTTAAAAAAATATTTTTATATTAATATTTCAAAT
Found at i:411720 original size:13 final size:13
Alignment explanation
Indices: 411702--411726 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
411692 CATAAAGTGT
411702 TGTATCGATACAA
1 TGTATCGATACAA
411715 TGTATCGATACA
1 TGTATCGATACA
411727 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:411742 original size:32 final size:33
Alignment explanation
Indices: 411682--411747 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
411672 TTCAACGATT
411682 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
411715 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
411747 T
1 T
411748 TTAAGCTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.59
33 13 0.41
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:411863 original size:52 final size:52
Alignment explanation
Indices: 411821--411949 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
411811 CACTGATCTT
*
411821 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTACCCAAATGTATCGATACACTATAAAA
* **
411873 TGTATCGATACATGCAGGCAAATTTACCTAGTTGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTACCCAAATGTATCGATACACTATAAAA
411925 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
411950 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTACCCAAATGTATCGATACACTATAAAA
Found at i:415655 original size:25 final size:24
Alignment explanation
Indices: 415621--415668 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
415611 TAAACACTTA
*
415621 TTTTGGATAAAGATGCATTGTAAC
1 TTTTGGATAAAGATGCACTGTAAC
*
415645 TTTTGGGATAAGGATGCACTGTAA
1 TTTT-GGATAAAGATGCACTGTAA
415669 TTTATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.35
Consensus pattern (24 bp):
TTTTGGATAAAGATGCACTGTAAC
Found at i:415719 original size:65 final size:65
Alignment explanation
Indices: 415610--415732 Score: 201
Period size: 65 Copynumber: 1.9 Consensus size: 65
415600 TCATGTGCAG
* *
415610 ATAAACACTTATTTTGGATAAAGATGCATTGTAACTTTTGGGATAAGGATGCACTGTAATTTATA
1 ATAAACACTTATCTTGGATAAAAATGCATTGTAACTTTTGGGATAAGGATGCACTGTAATTTATA
* * *
415675 ATAAGCACTTATCTTGGATAAAAATGCATTGTAGCTTTTGGGATAAGGATGCATTGTA
1 ATAAACACTTATCTTGGATAAAAATGCATTGTAACTTTTGGGATAAGGATGCACTGTA
415733 GTTTTTAGTA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 53 1.00
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (65 bp):
ATAAACACTTATCTTGGATAAAAATGCATTGTAACTTTTGGGATAAGGATGCACTGTAATTTATA
Found at i:420657 original size:2 final size:2
Alignment explanation
Indices: 420650--420676 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
420640 TTATATTGTG
420650 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
420677 GTAATCTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:420821 original size:44 final size:44
Alignment explanation
Indices: 420768--420856 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
420758 GGGTGGTACT
420768 TGGGCACTTTTTGCCCATAAATGCACGTGTGGGTGCTGTTTGGG
1 TGGGCACTTTTTGCCCATAAATGCACGTGTGGGTGCTGTTTGGG
420812 TGGGCACTTTTTGCCCATAAATGCACGTGTGGGTGCTGTTTGGG
1 TGGGCACTTTTTGCCCATAAATGCACGTGTGGGTGCTGTTTGGG
420856 T
1 T
420857 AGCACCTCAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.13, C:0.18, G:0.34, T:0.35
Consensus pattern (44 bp):
TGGGCACTTTTTGCCCATAAATGCACGTGTGGGTGCTGTTTGGG
Found at i:421974 original size:34 final size:34
Alignment explanation
Indices: 421931--421995 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
421921 ACCGAGCACG
*
421931 GACAACTATTGGTTCTTGTTTGGAGCCATCTGAT
1 GACAACTATTGGTTCTTGTTTGAAGCCATCTGAT
*
421965 GACAACTATTGGTTTTTGTTTGAAGCCATCT
1 GACAACTATTGGTTCTTGTTTGAAGCCATCT
421996 AAAGCCCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (34 bp):
GACAACTATTGGTTCTTGTTTGAAGCCATCTGAT
Found at i:422414 original size:24 final size:25
Alignment explanation
Indices: 422387--422485 Score: 73
Period size: 24 Copynumber: 3.9 Consensus size: 25
422377 AATAACGTAT
422387 TAAAAAA-TAAATAATTTTTTAAAG
1 TAAAAAATTAAATAATTTTTTAAAG
* *
422411 TAAAAAGATTAGATAATTTCTTTTGAAAA
1 TAAAAA-ATTAAATAA-TT-TTTT-AAAG
* *
422440 TGAAAAATT-AATTA-TTTTTAAACG
1 TAAAAAATTAAATAATTTTTTAAA-G
422464 -AAAAAATCTAAAT-ATTTTTTAA
1 TAAAAAAT-TAAATAATTTTTTAA
422486 TTTAATATTA
Statistics
Matches: 59, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
23 9 0.15
24 12 0.20
25 12 0.20
26 6 0.10
27 5 0.08
28 7 0.12
29 8 0.14
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (25 bp):
TAAAAAATTAAATAATTTTTTAAAG
Found at i:422798 original size:23 final size:21
Alignment explanation
Indices: 422758--422799 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
422748 ATTTTTTATT
*
422758 TAAATTTAATTATAAAATATA
1 TAAATTTAATAATAAAATATA
422779 TAAATATTAATAATTAAAATA
1 TAAAT-TTAATAA-TAAAATA
422800 AAATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAATAATAAAATATA
Found at i:422840 original size:13 final size:14
Alignment explanation
Indices: 422822--422854 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
422812 TTTTATTAAT
422822 TATAAATAATA-AA
1 TATAAATAATATAA
422835 TATAAATAATATAA
1 TATAAATAATATAA
422849 -ATAAAT
1 TATAAAT
422855 TAAATCAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 17 0.89
14 2 0.11
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TATAAATAATATAA
Found at i:423400 original size:14 final size:16
Alignment explanation
Indices: 423369--423419 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
423359 AAAAAATTAA
423369 TTTTATAAATAAATTT
1 TTTTATAAATAAATTT
*
423385 TTTTATAAA-ATA-TT
1 TTTTATAAATAAATTT
*
423399 TTTTA-AAGTAAAATTT
1 TTTTATAAAT-AAATTT
423415 TTTTA
1 TTTTA
423420 CGAATATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 2 0.07
14 7 0.24
15 4 0.14
16 16 0.55
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
TTTTATAAATAAATTT
Found at i:425903 original size:20 final size:21
Alignment explanation
Indices: 425853--425903 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 21
425843 AAGAACTAAT
*
425853 AATT-AATATTTTAATTGTTA
1 AATTAAATATTTTAAATGTTA
425873 AA-TAAAT-TTTTAAAT-TTA
1 AATTAAATATTTTAAATGTTA
425891 AATTAAATATTTT
1 AATTAAATATTTT
425904 TTATTTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 5 0.19
19 13 0.48
20 9 0.33
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
AATTAAATATTTTAAATGTTA
Found at i:425948 original size:121 final size:124
Alignment explanation
Indices: 425849--426146 Score: 322
Period size: 122 Copynumber: 2.5 Consensus size: 124
425839 TTAAAAGAAC
*
425849 TAATAATTAATATTTTAA-TTGTTAAATAAATTTTTAAATTTAAATTAAATA-T-TTTTTA-TTT
1 TAATAATTAATATTTTAATTTGTTAAATAAATTTTTAAACTT-AATTAAATATTATTTTTATTTT
* *
425910 ATTAAAATATGATAAAAAACTTTTTATTTTTATTTTAAATTTTTTATTTGTAGAAAAATA
65 ATTAAAAAATAATAAAAAACTTTTTATTTTTATTTTAAATTTTTTATTTGTAGAAAAATA
* *
425970 TAATAATTAATATTTTAATTTGTTAGATAATTTTTTAAACTTAATTAAATATTATTTTTATTTTA
1 TAATAATTAATATTTTAATTTGTTAAATAAATTTTTAAACTTAATTAAATATTATTTTTATTTTA
** *
426035 TTAAAAAATAATAAATATAAAC----CCTTTTTAATTT-AATTTTTTATTT-T----AAA-A
66 TTAAAAAATAAT-AA-A-AAACTTTTTATTTTTATTTTAAATTTTTTATTTGTAGAAAAATA
* * *
426086 -AATAATTAATATTTTAATTTATTAATGTAAATTTTTATAAAGTTAATTAAATATTATTTTT
1 TAATAATTAATATTTTAATTTGTTAA-ATAAA-TTTT-TAAACTTAATTAAATATTATTTTT
426147 TATTAAAAAA
Statistics
Matches: 154, Mismatches: 13, Indels: 23
0.81 0.07 0.12
Matches are distributed among these distances:
115 23 0.15
116 4 0.03
117 7 0.05
118 23 0.15
121 28 0.18
122 33 0.21
123 15 0.10
124 14 0.09
125 2 0.01
126 1 0.01
127 4 0.03
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.53
Consensus pattern (124 bp):
TAATAATTAATATTTTAATTTGTTAAATAAATTTTTAAACTTAATTAAATATTATTTTTATTTTA
TTAAAAAATAATAAAAAACTTTTTATTTTTATTTTAAATTTTTTATTTGTAGAAAAATA
Found at i:426270 original size:21 final size:21
Alignment explanation
Indices: 426246--426285 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
426236 CATGACCATT
426246 TTTTTAAAATTTAA-ATTTTTA
1 TTTTTAAAA-TTAATATTTTTA
*
426267 TTTTTATAATTAATATTTT
1 TTTTTAAAATTAATATTTT
426286 AAATTATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTAAAATTAATATTTTTA
Found at i:426354 original size:22 final size:22
Alignment explanation
Indices: 426320--426366 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
426310 AAATTTCATA
*
426320 AAAATAAATTAAATTA-ATTTT
1 AAAATAAAATAAATTAGATTTT
426341 AAAATAAAAATAAATTAGATTTT
1 AAAAT-AAAATAAATTAGATTTT
426364 AAA
1 AAA
426367 TTTTATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.22
22 10 0.43
23 8 0.35
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAATAAAATAAATTAGATTTT
Found at i:426367 original size:22 final size:21
Alignment explanation
Indices: 426299--426367 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 21
426289 TTATATATAA
**
426299 TAAATAAAAATAAATT--TCA
1 TAAATAAAAATAAATTAATTT
426318 TAAA-AATAAATTAAATTAATTT
1 TAAATAA-AAA-TAAATTAATTT
426340 TAAAATAAAAATAAATTAGATTT
1 T-AAATAAAAATAAATTA-ATTT
426363 TAAAT
1 TAAAT
426368 TTTATTTAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
18 2 0.05
19 7 0.17
20 6 0.15
22 13 0.32
23 11 0.27
24 2 0.05
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (21 bp):
TAAATAAAAATAAATTAATTT
Found at i:426865 original size:14 final size:15
Alignment explanation
Indices: 426848--426876 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
426838 ACTTATTTTG
426848 AAAAATAT-TTTACA
1 AAAAATATATTTACA
426862 AAAAATATATTTACA
1 AAAAATATATTTACA
426877 GAATTAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAAATATATTTACA
Found at i:427410 original size:6 final size:7
Alignment explanation
Indices: 427395--427535 Score: 60
Period size: 6 Copynumber: 21.9 Consensus size: 7
427385 CTAGTTATTT
427395 TTATATA
1 TTATATA
427402 TTATA-A
1 TTATATA
427408 TTATAT-
1 TTATATA
*
427414 TTAAAATA
1 TT-ATATA
427422 TTATATA
1 TTATATA
427429 TT-TATA
1 TTATATA
* *
427435 -TAAATT
1 TTATATA
427441 TTAAATATA
1 TT--ATATA
427450 TTATATA
1 TTATATA
* *
427457 -AATTTA
1 TTATATA
*
427463 ATATAT-
1 TTATATA
*
427469 TTGTATA
1 TTATATA
427476 TTA-ATA
1 TTATATA
**
427482 TCGTAT-
1 TTATATA
427488 TTATAT-
1 TTATATA
427494 TT-TA-A
1 TTATATA
427499 TTAT-T-
1 TTATATA
427504 TTATATA
1 TTATATA
427511 TTATA-A
1 TTATATA
427517 TTATATA
1 TTATATA
*
427524 ATATA-A
1 TTATATA
427530 TTATAT
1 TTATAT
427536 TGTATTGAAA
Statistics
Matches: 98, Mismatches: 19, Indels: 34
0.65 0.13 0.23
Matches are distributed among these distances:
5 9 0.09
6 45 0.46
7 37 0.38
8 2 0.02
9 5 0.05
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (7 bp):
TTATATA
Found at i:427414 original size:11 final size:10
Alignment explanation
Indices: 427397--427534 Score: 54
Period size: 9 Copynumber: 15.0 Consensus size: 10
427387 AGTTATTTTT
427397 ATATATTATA
1 ATATATTATA
427407 ATTATATT-TA
1 A-TATATTATA
*
427417 AAATATTAT-
1 ATATATTATA
427426 ATAT-TTAT-
1 ATATATTATA
* *
427434 ATAAATTTTAA
1 ATATATTAT-A
427445 ATATATTAT-
1 ATATATTATA
*
427454 ATAAATT-TA
1 ATATATTATA
427463 ATATATT-T-
1 ATATATTATA
*
427471 GTATA-T-TA
1 ATATATTATA
**
427479 ATATCGTAT-
1 ATATATTATA
* *
427488 TTATATTTTA
1 ATATATTATA
*
427498 AT-TATT-TT
1 ATATATTATA
427506 ATATATTATA
1 ATATATTATA
427516 AT-TA-TATA
1 ATATATTATA
427524 ATATAATTATA
1 ATAT-ATTATA
427535 TTGTATTGAA
Statistics
Matches: 95, Mismatches: 18, Indels: 29
0.67 0.13 0.20
Matches are distributed among these distances:
7 2 0.02
8 24 0.25
9 41 0.43
10 11 0.12
11 17 0.18
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (10 bp):
ATATATTATA
Found at i:427433 original size:35 final size:34
Alignment explanation
Indices: 427394--427522 Score: 100
Period size: 35 Copynumber: 3.6 Consensus size: 34
427384 TCTAGTTATT
427394 TTTATATATTATAATTATATTTAAAATATTATATA
1 TTTATATATTATAATTATATTTAAAAT-TTATATA
* *
427429 TTTATATAAATTTTAAATATATTATATAAATTTAATATA
1 TTTATAT--ATTATAATTATATT-TA-AAATTT-ATATA
* ** * *
427468 TTTGTATATTA-ATATCGTATTTATATTTTA-ATTA
1 TTTATATATTATA-ATTATATTTAAAATTTATA-TA
427502 TTTTATATATTATAATTATAT
1 -TTTATATATTATAATTATAT
427523 AATATAATTA
Statistics
Matches: 73, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
33 1 0.01
34 3 0.04
35 26 0.36
36 4 0.05
37 20 0.27
38 4 0.05
39 15 0.21
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.56
Consensus pattern (34 bp):
TTTATATATTATAATTATATTTAAAATTTATATA
Found at i:427438 original size:20 final size:19
Alignment explanation
Indices: 427399--427475 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 19
427389 TTATTTTTAT
*
427399 ATATTATA-ATTATATTTAAA
1 ATATTATATATT-TATAT-AA
427419 ATATTATATATTTATATAA
1 ATATTATATATTTATATAA
* *
427438 ATTTTAAATATATTATATAA
1 ATATTATATAT-TTATATAA
*
427458 AT-TTAATATATTTGTATA
1 ATATT-ATATATTTATATA
427476 TTAATATCGT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
19 19 0.39
20 27 0.55
21 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (19 bp):
ATATTATATATTTATATAA
Found at i:427522 original size:13 final size:13
Alignment explanation
Indices: 427504--427535 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
427494 TTTAATTATT
*
427504 TTATATATTATAA
1 TTATATAATATAA
427517 TTATATAATATAA
1 TTATATAATATAA
427530 TTATAT
1 TTATAT
427536 TGTATTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTATATAATATAA
Found at i:427832 original size:16 final size:15
Alignment explanation
Indices: 427807--427838 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
427797 TATTTATATT
427807 TTAAAAATGATTTTG
1 TTAAAAATGATTTTG
427822 TTAACAAATGATTTTG
1 TTAA-AAATGATTTTG
427838 T
1 T
427839 GGTATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (15 bp):
TTAAAAATGATTTTG
Found at i:435814 original size:17 final size:17
Alignment explanation
Indices: 435792--435826 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
435782 CAACATTAGT
*
435792 AAACCATATAATAACAC
1 AAACCATATAACAACAC
435809 AAACCATATAACAACAC
1 AAACCATATAACAACAC
435826 A
1 A
435827 TCTTTAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.60, C:0.26, G:0.00, T:0.14
Consensus pattern (17 bp):
AAACCATATAACAACAC
Found at i:436241 original size:12 final size:12
Alignment explanation
Indices: 436224--436249 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
436214 CTCCCGTTTG
436224 TCGCAACATAGC
1 TCGCAACATAGC
436236 TCGCAACATAGC
1 TCGCAACATAGC
436248 TC
1 TC
436250 ATATGCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.35, G:0.15, T:0.19
Consensus pattern (12 bp):
TCGCAACATAGC
Found at i:437419 original size:153 final size:153
Alignment explanation
Indices: 437148--437435 Score: 337
Period size: 153 Copynumber: 1.9 Consensus size: 153
437138 GTATACTTTC
* * * * * *
437148 GATGTGAAAGTATCTTGGTAATCCTAAAGGACACGAAAAGATAATAAAAGGGTGAACCTATTCTA
1 GATGTGAAAATAACTCGGTAACCCTAAAGGACACGAAAAGATAATAAAAGGATGAACCTATCCTA
* * * * * * *
437213 CATGTACACCTTTGGCATAAAAGCAACCCGATAACGACTTAATACTTAATTCTAGAGAAATTATC
66 AATGCACACCTTTGGCATAAAAGCAACCCGATAACGACTTAAGACTCAATTCTAAAAAAATTACC
437278 AAAATGCCTCCAGGTATTTTTTT
131 AAAATGCCTCCAGGTATTTTTTT
* * *
437301 GATGTGAAAATAACTCGGTAACCCTAAAGGAGATGAAAAGATAATTAAAGGATGAACCTATCCTA
1 GATGTGAAAATAACTCGGTAACCCTAAAGGACACGAAAAGATAATAAAAGGATGAACCTATCCTA
* * * * * * *
437366 AATGCATACCTTTGGCATCAAAGTGATCCTG-TAACGAAC-TAGGACTCATTTCTAAAAAAATTA
66 AATGCACACCTTTGGCATAAAAG-CAACCCGATAACG-ACTTAAGACTCAATTCTAAAAAAATTA
437429 CCAAAAT
129 CCAAAAT
437436 ACTCCTAAGG
Statistics
Matches: 110, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
153 104 0.95
154 6 0.05
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (153 bp):
GATGTGAAAATAACTCGGTAACCCTAAAGGACACGAAAAGATAATAAAAGGATGAACCTATCCTA
AATGCACACCTTTGGCATAAAAGCAACCCGATAACGACTTAAGACTCAATTCTAAAAAAATTACC
AAAATGCCTCCAGGTATTTTTTT
Found at i:439912 original size:66 final size:65
Alignment explanation
Indices: 439824--440011 Score: 205
Period size: 67 Copynumber: 2.8 Consensus size: 65
439814 GACTAGGATG
* * *
439824 AAACTTAAGTAAAAAAAGGTGTTGACCAAGGTAAAATAGATAAAGTCACTAAAAAAGACCAAGGC
1 AAACCTAAGT-AAAAAAGGTGTTGACCAAGGTAAAATCGATAAAGTCACTAAAAAAGACCAACGC
439889 A
65 A
** * * * * *
439890 AAACCTAAGTTGAAAAGAGTGTTGATCAAAGCAAAATCGATAAAGTTAACTAAAAGAGACCAACG
1 AAACCTAAGTAAAAAAG-GTGTTGACCAAGGTAAAATCGATAAAG-TCACTAAAAAAGACCAACG
439955 CA
64 CA
* * * *
439957 GAACCTAAGTAAAAAAGGATGTTGTCCAGGGTGAAATCGATAAAGTCAACTAAAA
1 AAACCTAAGTAAAAAAGG-TGTTGACCAAGGTAAAATCGATAAAGTC-ACTAAAA
440012 GTGACTAGGA
Statistics
Matches: 98, Mismatches: 20, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
65 5 0.05
66 34 0.35
67 59 0.60
ACGTcount: A:0.49, C:0.13, G:0.19, T:0.18
Consensus pattern (65 bp):
AAACCTAAGTAAAAAAGGTGTTGACCAAGGTAAAATCGATAAAGTCACTAAAAAAGACCAACGCA
Found at i:440047 original size:133 final size:132
Alignment explanation
Indices: 439829--440297 Score: 321
Period size: 131 Copynumber: 3.5 Consensus size: 132
439819 GGATGAAACT
* * * ** * *
439829 TAAGTAAAAAAAGGTGTTGACCAAGGTAAAATAGATAAAGTC-ACTAAAAAAGACCAAGG-CAAA
1 TAAGT-AAAAAAGGTGTTGACCAGGGTGAAATCGATAAAGTCAACTAAAAGTGA-CTAGGATAAA
* * *
439892 ACCTAAGTTGAAAAGAGTGTTGA-TCAAAGCAAAA-TCGATAAAGTTAACTAAAAGAGACCAACG
64 ACCTAAG-TCAAAAGAGAGTTGACT-AAAGCAAAACT-GATAAAGTCAACTAAAAGAGA-CAA-G
* *
439955 CA-GAA-CC
124 AATAAAGCC
*
439962 TAAGTAAAAAAGGATGTTGTCCAGGGTGAAATCGATAAAGTCAACTAAAAGTGACTAGGATAAAA
1 TAAGTAAAAAAGG-TGTTGACCAGGGTGAAATCGATAAAGTCAACTAAAAGTGACTAGGATAAAA
* * ** ** * *
440027 CTTAAGTCAAAATAGAGTTGACTAGGGTGAAACTGATAAAGTCAACTAAAAGTGACTAGAATAAA
65 CCTAAGTCAAAAGAGAGTTGACTAAAGCAAAACTGATAAAGTCAACTAAAAGAGACAAGAATAAA
*
440092 GCT
130 GCC
** * * *
440095 TAAGTCGAAATGG-GTTGACCAGGGTGAAATCAATAAAGTCAACTAAAAGTGACTAAGATAAAAC
1 TAAGTAAAAAAGGTGTTGACCAGGGTGAAATCGATAAAGTCAACTAAAAGTGACTAGGATAAAAC
* * * ** * * * * *
440159 CTAAGTTGAAATG-GCA-TTGATTAGGGC-GAAGTCGATAAAGTCAACTAAAAGTGACTAGGATA
66 CTAAG-TCAAAAGAG-AGTTGACTAAAGCAAAACT-GATAAAGTCAACTAAAAGAGACAAGAATA
*
440221 AAACC
128 AAGCC
** * * * * * * * *
440226 TAAGTCGAAATGG-GATTAACTAAGGCGAAGTCGATAAATTTAACTAAAAGTGACTAGGATAAAA
1 TAAGTAAAAAAGGTG-TTGACCAGGGTGAAATCGATAAAGTCAACTAAAAGTGACTAGGATAAAA
440290 CCTAAGTC
65 CCTAAGTC
440298 GAAATAGGTT
Statistics
Matches: 276, Mismatches: 49, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
130 3 0.01
131 110 0.40
132 63 0.23
133 80 0.29
134 20 0.07
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.21
Consensus pattern (132 bp):
TAAGTAAAAAAGGTGTTGACCAGGGTGAAATCGATAAAGTCAACTAAAAGTGACTAGGATAAAAC
CTAAGTCAAAAGAGAGTTGACTAAAGCAAAACTGATAAAGTCAACTAAAAGAGACAAGAATAAAG
CC
Found at i:440069 original size:66 final size:65
Alignment explanation
Indices: 439984--440367 Score: 443
Period size: 66 Copynumber: 5.8 Consensus size: 65
439974 GATGTTGTCC
* *
439984 AGGGTGAAATCGATAAAGTCAACTAAAAGTGACTAGGATAAAACTTAAGTCAAAATAGAGTTGAC
1 AGGGTGAAATCGATAAAGTCAACTAAAAGTGACTAGGATAAAACCTAAGTCGAAAT-GAGTTGAC
440049 T
65 T
* * * *
440050 AGGGTGAAA-CTGATAAAGTCAACTAAAAGTGACTAGAATAAAGCTTAAGTCGAAATGGGTTGAC
1 AGGGTGAAATC-GATAAAGTCAACTAAAAGTGACTAGGATAAAACCTAAGTCGAAATGAGTTGAC
*
440114 C
65 T
* * *
440115 AGGGTGAAATCAATAAAGTCAACTAAAAGTGACTAAGATAAAACCTAAGTTGAAATG-GCATTGA
1 AGGGTGAAATCGATAAAGTCAACTAAAAGTGACTAGGATAAAACCTAAGTCGAAATGAG--TTGA
*
440179 TT
64 CT
* * * *
440181 AGGGCGAAGTCGATAAAGTCAACTAAAAGTGACTAGGATAAAACCTAAGTCGAAATGGGATTAAC
1 AGGGTGAAATCGATAAAGTCAACTAAAAGTGACTAGGATAAAACCTAAGTCGAAATGAG-TTGAC
440246 T
65 T
* * * * *
440247 AAGGCGAAGTCGATAAATTTAACTAAAAGTGACTAGGATAAAACCTAAGTCGAAAT-AGGTTGGA
1 AGGGTGAAATCGATAAAGTCAACTAAAAGTGACTAGGATAAAACCTAAGTCGAAATGA-GTT-GA
*
440311 CC
64 CT
* ** *
440313 AGGAT-ATAGCCGATAAAGTCAACTAAAAGTGACTAAGATAAAACCTAAGTCGAAA
1 AGGGTGA-AATCGATAAAGTCAACTAAAAGTGACTAGGATAAAACCTAAGTCGAAA
440368 AGCCGATAAA
Statistics
Matches: 277, Mismatches: 33, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
64 1 0.00
65 60 0.22
66 215 0.78
67 1 0.00
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.21
Consensus pattern (65 bp):
AGGGTGAAATCGATAAAGTCAACTAAAAGTGACTAGGATAAAACCTAAGTCGAAATGAGTTGACT
Found at i:440085 original size:34 final size:34
Alignment explanation
Indices: 439984--440085 Score: 108
Period size: 32 Copynumber: 3.1 Consensus size: 34
439974 GATGTTGTCC
439984 AGGGTGAAA-TCGATAAAGTCAACTAAAAGTGACT
1 AGGGTGAAACT-GATAAAGTCAACTAAAAGTGACT
* *
440018 AGGATAAAACT--T-AAGTCAA--AATAGAGTTGACT
1 AGGGTGAAACTGATAAAGTCAACTAA-A-AG-TGACT
440050 AGGGTGAAACTGATAAAGTCAACTAAAAGTGACT
1 AGGGTGAAACTGATAAAGTCAACTAAAAGTGACT
440084 AG
1 AG
440086 AATAAAGCTT
Statistics
Matches: 55, Mismatches: 4, Indels: 18
0.71 0.05 0.23
Matches are distributed among these distances:
29 2 0.04
30 1 0.02
31 9 0.16
32 15 0.27
34 15 0.27
35 10 0.18
36 1 0.02
37 2 0.04
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.22
Consensus pattern (34 bp):
AGGGTGAAACTGATAAAGTCAACTAAAAGTGACT
Found at i:440140 original size:131 final size:131
Alignment explanation
Indices: 439977--440367 Score: 477
Period size: 131 Copynumber: 3.0 Consensus size: 131
439967 AAAAAAGGAT
* * *
439977 GTTGTCCAGGGTGAAATCGATAAAGTCAACTAAAAGTGACTAGGATAAAACTTAAGTCAAAATAG
1 GTTGACCAGGGTGAAATCGATAAAGTCAACTAAAAGTGACTAGGATAAAACCTAAGTCGAAATAG
* *
440042 AGTTGACTAGGGTGAAACTGATAAAGTCAACTAAAAGTGACTAGAATAAAGCTTAAGTCGAAATG
66 AGTTGACTAGGGTGAAACTGATAAAGTCAACTAAAAGTGACTAGAATAAAACCTAAGTCGAAATG
440107 G
131 G
* * * *
440108 GTTGACCAGGGTGAAATCAATAAAGTCAACTAAAAGTGACTAAGATAAAACCTAAGTTGAAATGG
1 GTTGACCAGGGTGAAATCGATAAAGTCAACTAAAAGTGACTAGGATAAAACCTAAGTCGAAATAG
* * * *
440173 CA-TTGATTAGGGCG-AAGTCGATAAAGTCAACTAAAAGTGACTAGGATAAAACCTAAGTCGAAA
66 -AGTTGACTAGGGTGAAACT-GATAAAGTCAACTAAAAGTGACTAGAATAAAACCTAAGTCGAAA
440236 TGG
129 TGG
* * * * * * *
440239 GATTAACTAAGGCGAAGTCGATAAATTTAACTAAAAGTGACTAGGATAAAACCTAAGTCGAAATA
1 G-TTGACCAGGGTGAAATCGATAAAGTCAACTAAAAGTGACTAGGATAAAACCTAAGTCGAAATA
* * * *
440304 G-GTTGGACCAGGAT-ATAGCCGATAAAGTCAACTAAAAGTGACTA-AGATAAAACCTAAGTCGA
65 GAGTT-GACTAGGGTGA-AACTGATAAAGTCAACTAAAAGTGACTAGA-ATAAAACCTAAGTCGA
440366 AA
127 AA
440368 AGCCGATAAA
Statistics
Matches: 220, Mismatches: 32, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
130 3 0.01
131 115 0.52
132 101 0.46
133 1 0.00
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (131 bp):
GTTGACCAGGGTGAAATCGATAAAGTCAACTAAAAGTGACTAGGATAAAACCTAAGTCGAAATAG
AGTTGACTAGGGTGAAACTGATAAAGTCAACTAAAAGTGACTAGAATAAAACCTAAGTCGAAATG
G
Found at i:440410 original size:48 final size:47
Alignment explanation
Indices: 440320--440415 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 47
440310 ACCAGGATAT
440320 AGCCGATAAAGTCAACTAAAAGTGACTAAGATAAAACCTAAGTCGAAA
1 AGCCGATAAAGTCAACTAAAAGTGACTAAGATAAAACCTAAGTC-AAA
* * * * **
440368 AGCCGATAAAGTTAATTAAAAGTGATTAGGATAAAATTTAAGTCAAA
1 AGCCGATAAAGTCAACTAAAAGTGACTAAGATAAAACCTAAGTCAAA
440415 A
1 A
440416 TGGGGTTAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
47 4 0.10
48 38 0.90
ACGTcount: A:0.50, C:0.11, G:0.17, T:0.22
Consensus pattern (47 bp):
AGCCGATAAAGTCAACTAAAAGTGACTAAGATAAAACCTAAGTCAAA
Found at i:440495 original size:180 final size:179
Alignment explanation
Indices: 440191--440547 Score: 468
Period size: 180 Copynumber: 2.0 Consensus size: 179
440181 AGGGCGAAGT
* * * *
440191 CGATAAAGTCAACTAAAAGTGACTAGGATAAAACCTAAGTCGAAATGGGATTAACTAAGGCGAAG
1 CGATAAAGTCAACTAAAAGTGACTAGGATAAAACCTAAGTCAAAATGGGATTAACCAAGGCAAAA
* * *
440256 TCGATAAATTTAACTAAAAGTGACTAGGATAAAACCTAAGTCGAAATAGGTTGGACCAGGA-TAT
66 TCGATAAAGTTAACTAAAAGTGACTACGATAAAACCTAAGTCGAAATAGGTTGGACCAGGACGA-
* * *
440320 AGCCGATAAAGTCAACTAAAAGTGACTAAGATAAAACCTAAGTCGAAAAGC
130 AACCGATAAAGTAAACTAAAAGTGACTAAGACAAAACCTAAGTC-AAAAGC
* * * ** * *
440371 CGATAAAGTTAATTAAAAGTGATTAGGATAAAATTTAAGTCAAAATGGGGTTAACCAGGGCAAAA
1 CGATAAAGTCAACTAAAAGTGACTAGGATAAAACCTAAGTCAAAATGGGATTAACCAAGGCAAAA
*
440436 TTGATAAAGTTAACTAAAAAG-GACTACGATAAAACCTAAGTCGAAATTAGGTT-GACCAGGACG
66 TCGATAAAGTTAACT-AAAAGTGACTACGATAAAACCTAAGTCGAAA-TAGGTTGGACCAGGACG
* * *
440499 AAACTGATAAAGTAAACTAAAAGTGACTAGGGCAAAACCTAAGTCAAAA
129 AAACCGATAAAGTAAACTAAAAGTGACTAAGACAAAACCTAAGTCAAAA
440548 TGGGGTTGAG
Statistics
Matches: 153, Mismatches: 21, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
179 4 0.03
180 137 0.90
181 12 0.08
ACGTcount: A:0.46, C:0.13, G:0.20, T:0.21
Consensus pattern (179 bp):
CGATAAAGTCAACTAAAAGTGACTAGGATAAAACCTAAGTCAAAATGGGATTAACCAAGGCAAAA
TCGATAAAGTTAACTAAAAGTGACTACGATAAAACCTAAGTCGAAATAGGTTGGACCAGGACGAA
ACCGATAAAGTAAACTAAAAGTGACTAAGACAAAACCTAAGTCAAAAGC
Found at i:440555 original size:66 final size:66
Alignment explanation
Indices: 440372--440556 Score: 219
Period size: 66 Copynumber: 2.8 Consensus size: 66
440362 TCGAAAAGCC
* * ** * * *
440372 GATAAAGTTAATTAAAAGTGATTAGGATAAAATTTAAGTCAAAATGGGGTTAACCAGGGCAAAAT
1 GATAAAGTTAACTAAAAGTGACTAGGATAAAACCTAAGTCAAAATGGGGTTGACCAGGACAAAAC
440437 T
66 T
* * ** *
440438 GATAAAGTTAACTAAAAAG-GACTACGATAAAACCTAAGTCGAAATTAGGTTGACCAGGACGAAA
1 GATAAAGTTAACT-AAAAGTGACTAGGATAAAACCTAAGTCAAAATGGGGTTGACCAGGACAAAA
440502 CT
65 CT
* **
440504 GATAAAGTAAACTAAAAGTGACTAGGGCAAAACCTAAGTCAAAATGGGGTTGA
1 GATAAAGTTAACTAAAAGTGACTAGGATAAAACCTAAGTCAAAATGGGGTTGA
440557 GTGACATTTG
Statistics
Matches: 98, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
65 5 0.05
66 88 0.90
67 5 0.05
ACGTcount: A:0.45, C:0.11, G:0.22, T:0.22
Consensus pattern (66 bp):
GATAAAGTTAACTAAAAGTGACTAGGATAAAACCTAAGTCAAAATGGGGTTGACCAGGACAAAAC
T
Found at i:441154 original size:75 final size:75
Alignment explanation
Indices: 441057--441481 Score: 328
Period size: 76 Copynumber: 5.7 Consensus size: 75
441047 ACACAATAAG
* * * *
441057 GAATATGT-AGTTTCTAAAATTTTTATCAACAGCTAAAATAAACTGATAATATGCTGAAGGAAAT
1 GAATATGTGA-TTTCTAAAATTTTCATCAACAGCCAAAACAAACTGATAATAGGCTGAAGGAAAT
441121 AACATGATGGA
65 AACATGATGGA
* * * * * *
441132 GAATATGTGATTTCTAAAATTTTCATTAATAGCCAAAACAAATTGATAA-AGGCTAAAGAAAAGG
1 GAATATGTGATTTCTAAAATTTTCATCAACAGCCAAAACAAACTGATAATAGGCTGAAGGAAA-T
441196 AACATGATGGA
65 AACATGATGGA
* * * * * * * *
441207 GAATATATGGTTTCTAAAATTTCCCTCAACAGCTAACATAAATTGATAATAGGCTGAAGGAAAAT
1 GAATATGTGATTTCTAAAATTTTCATCAACAGCCAAAACAAACTGATAATAGGCTGAAGG-AAAT
441272 AACATGAT-GA
65 AACATGATGGA
* * * * * * *
441282 GGAATATGTGATTTCTAAAATTTTTATTAATAGCCAAAACAAACTGATGACA-ACTTAAAGGAAA
1 -GAATATGTGATTTCTAAAATTTTCATCAACAGCCAAAACAAACTGATAATAGGC-TGAAGGAAA
*
441346 GGAACATGATAGGA
64 -TAACATGAT-GGA
* * * * * * * *
441360 -AATATGTGTTTTCTATAATTTCCATTAACAACCGAAACAAATTGATAACT-GGTTGAAGGAAAG
1 GAATATGTGATTTCTAAAATTTTCATCAACAGCCAAAACAAACTGATAA-TAGGCTGAAGGAAA-
*
441423 AAACATGAT-GA
64 TAACATGATGGA
* ** * * *
441434 -AACATACGATTTCTACAATTTCTC-TCAACAACCAAAATAAACTGATAA
1 GAATATGTGATTTCTAAAATTT-TCATCAACAGCCAAAACAAACTGATAA
441482 CCAGTTAGAG
Statistics
Matches: 276, Mismatches: 62, Indels: 25
0.76 0.17 0.07
Matches are distributed among these distances:
74 48 0.17
75 99 0.36
76 124 0.45
77 3 0.01
78 2 0.01
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.28
Consensus pattern (75 bp):
GAATATGTGATTTCTAAAATTTTCATCAACAGCCAAAACAAACTGATAATAGGCTGAAGGAAATA
ACATGATGGA
Found at i:441420 original size:152 final size:151
Alignment explanation
Indices: 441057--441433 Score: 428
Period size: 152 Copynumber: 2.5 Consensus size: 151
441047 ACACAATAAG
* * ** * * * * * *
441057 GAATATGTAGTTTCTAAAATTTTTATCAACAGCTAAAATAAACTGATAATATGCTGAAGG-AAAT
1 GAATATATGGTTTCTAAAATTTCCATCAACACCGAACACAAATTGATAATAGGCTGAAGGAAAAT
*
441121 AACATGATG-GAGAATATGTGATTTCTAAAATTTTCATTAATAGCCAAAACAAATTGATAAAGGC
66 AACATGATGAGAGAATATGTGATTTCTAAAATTTTCATTAATAGCCAAAACAAACTGATAAA-GC
441185 TAAAGAAAAGGAACATGATGGA
130 TAAAGAAAAGGAACATGATGGA
* * * *
441207 GAATATATGGTTTCTAAAATTTCCCTCAACAGCTAACATAAATTGATAATAGGCTGAAGGAAAAT
1 GAATATATGGTTTCTAAAATTTCCATCAACACCGAACACAAATTGATAATAGGCTGAAGGAAAAT
*
441272 AACATGATGAG-GAATATGTGATTTCTAAAATTTTTATTAATAGCCAAAACAAACTGATGACAA-
66 AACATGATGAGAGAATATGTGATTTCTAAAATTTTCATTAATAGCCAAAACAAACTGAT-A-AAG
*
441335 CTTAAAGGAAAGGAACATGATAGGA
129 C-TAAAGAAAAGGAACATGAT-GGA
* * * * *
441360 -AATATGTGTTTTCTATAATTTCCATTAACAACCGAA-ACAAATTGATAACT-GGTTGAAGGAAA
1 GAATATATGGTTTCTAAAATTTCCATCAAC-ACCGAACACAAATTGATAA-TAGGCTGAAGGAAA
441422 GA-AACATGATGA
64 -ATAACATGATGA
441434 AACATACGAT
Statistics
Matches: 198, Mismatches: 20, Indels: 16
0.85 0.09 0.07
Matches are distributed among these distances:
150 52 0.26
151 59 0.30
152 76 0.38
153 11 0.06
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (151 bp):
GAATATATGGTTTCTAAAATTTCCATCAACACCGAACACAAATTGATAATAGGCTGAAGGAAAAT
AACATGATGAGAGAATATGTGATTTCTAAAATTTTCATTAATAGCCAAAACAAACTGATAAAGCT
AAAGAAAAGGAACATGATGGA
Found at i:444053 original size:21 final size:22
Alignment explanation
Indices: 444027--444080 Score: 101
Period size: 21 Copynumber: 2.5 Consensus size: 22
444017 TGGACATGTT
444027 AAAAATGCATGAAACATAAT-A
1 AAAAATGCATGAAACATAATAA
444048 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
444070 AAAAATGCATG
1 AAAAATGCATG
444081 GTCAAAGGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 20 0.62
22 12 0.38
ACGTcount: A:0.61, C:0.09, G:0.11, T:0.19
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:445040 original size:20 final size:20
Alignment explanation
Indices: 444993--445067 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
444983 AAAAAGACAT
*
444993 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
445012 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
445033 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
445053 AATGTATCGATACAT
1 AATGTATCGATACAT
445068 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:445061 original size:40 final size:39
Alignment explanation
Indices: 444990--445067 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
444980 GGTAAAAAGA
* *
444990 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
445029 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
445068 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:446061 original size:143 final size:144
Alignment explanation
Indices: 445593--446738 Score: 1618
Period size: 143 Copynumber: 8.0 Consensus size: 144
445583 TGAAAAGGGT
* * * **
445593 TGCCATTGACTTGCATGGGCTTTAAAAGG-GTGCCACTGACTTGCGTAGGCTTTGAAAGAATGCC
1 TGCCACTGACTTG--TGGGCTTTGAAAGGAGTGCCACTGACTT--GTGGGCTTTGAAAGGGTGCC
* * * * *
445657 ACTAACTCGTGGGCTTTGAAAGGA-TGCCACTAACTCGTGGGCTTTG-AAAGAGTGCCACTGACT
62 ACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
*
445720 TGTGGGCTTTGAAAAG-G
127 TGTGGGCTTTGAAAGGAG
* * * * * *
445737 TACCACTGACTTGCGTGAGATTTAAAAGGAGTGCCATTGACTTGTGTGGGCTTTAAAAGGGTGCC
1 TGCCACTGACTT--GTGGGCTTTGAAAGGAGTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCC
* * *
445802 ACTGACTTGTGGGCTTT-AAAAGAGTGCCACTGAATTGTGGGCTTTG-CAATAGTGCCACTGACT
62 ACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
445865 TGTGGGCTTCGAAAAG-G
127 TGTGGGCTTTGAAAGGAG
* *
445882 TGCCACTGACTTGTGGGCTCTGAAAGG-GTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
* * *
445946 ACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAATGCCACTAACTTGTG
66 ACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTG
446011 GGCTTTGAAAGGAG
131 GGCTTTGAAAGGAG
* *
446025 TGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACT
1 TGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACT
* * *
446089 GATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGTTTTGAAAGGAGTGCCACTGACTTGT
65 GACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGT
446154 GGGCTTTGAAAGG-G
130 GGGCTTTGAAAGGAG
* *
446168 TGCCACTGAGTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACT
1 TGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACT
* * * * *
446232 GATTTGTGGGATTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTCGT
65 GACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGT
*
446297 GGGCTTTGAAAAGAG
130 GGGCTTTGAAAGGAG
* *
446312 TGCCACTGATTTGTGGGTTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
* *
446377 ACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTG
66 ACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTG
*
446441 GGATTTGAAAGGAG
131 GGCTTTGAAAGGAG
*
446455 TGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
* * *
446520 ACTTGTGGGCTTTG-AAAGAGTGCCATTGATTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTG
66 ACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTG
446584 GGCTTTGAAAGGAG
131 GGCTTTGAAAGGAG
* * *
446598 TGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCATTA
1 TGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
* *
446663 ACTTGTGGGCTTTG-AAAGAGTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTG
66 ACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTG
446727 GGCTTTGAAAGG
131 GGCTTTGAAAGG
446739 GATGAACATT
Statistics
Matches: 918, Mismatches: 72, Indels: 25
0.90 0.07 0.02
Matches are distributed among these distances:
140 37 0.04
141 29 0.03
142 36 0.04
143 526 0.57
144 162 0.18
145 125 0.14
146 2 0.00
147 1 0.00
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (144 bp):
TGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
ACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTG
GGCTTTGAAAGGAG
Found at i:446737 original size:29 final size:29
Alignment explanation
Indices: 445593--446738 Score: 1639
Period size: 29 Copynumber: 39.9 Consensus size: 29
445583 TGAAAAGGGT
* *
445593 TGCCATTGACTTGCATGGGCTTTAAAAGG-G
1 TGCCACTGACTTG--TGGGCTTTGAAAGGAG
* *
445623 TGCCACTGACTTGCGTAGGCTTTGAAA-GAA
1 TGCCACTGACTT--GTGGGCTTTGAAAGGAG
* *
445653 TGCCACTAACTCGTGGGCTTTGAAAGGA-
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
445681 TGCCACTAACTCGTGGGCTTTGAAA-GAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
445709 TGCCACTGACTTGTGGGCTTTGAAAAG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * * *
445737 TACCACTGACTTGCGTGAGATTTAAAAGGAG
1 TGCCACTGACTT--GTGGGCTTTGAAAGGAG
* *
445768 TGCCATTGACTTGTGTGGGCTTTAAAAGG-G
1 TGCCACTGAC-T-TGTGGGCTTTGAAAGGAG
*
445798 TGCCACTGACTTGTGGGCTTT-AAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * *
445826 TGCCACTGAATTGTGGGCTTTGCAA-TAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
445854 TGCCACTGACTTGTGGGCTTCGAAAAG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
445882 TGCCACTGACTTGTGGGCTCTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
445910 TGCCACTAACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
445938 TGCCACTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * *
445967 TGCCACTGATTTGTGGGCTTTGAAAAGAA
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
445996 TGCCACTAACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
446025 TGCCACTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
446053 TGCCACTAACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
446082 TGCCACTGATTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
446111 TGCCACTGACTTGTGGGTTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
446140 TGCCACTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
446168 TGCCACTGAGTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
446196 TGCCACTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
446225 TGCCACTGATTTGTGGGATTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
446254 TGCCACTGACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
446283 TGCCACTGACTCGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
446312 TGCCACTGATTTGTGGGTTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
446341 TGCCACTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
446369 TGCCACTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
446397 TGCCACTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
446426 TGCCACTGATTTGTGGGATTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
446455 TGCCACTGACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
446484 TGCCACTGACTTGTGGGCTTTGAAAGGA-
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
446512 TGCCACTGACTTGTGGGCTTTGAAA-GAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
446540 TGCCATTGATTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
446569 TGCCACTGACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
446598 TGCCACTGACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
446627 TGCCACTGACTTGTGGGCTTTGAAAGGA-
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
446655 TGCCATTAACTTGTGGGCTTTGAAA-GAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
446683 TGCCACTGATTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
446712 TGCCACTGACTTGTGGGCTTTGAAAGG
1 TGCCACTGACTTGTGGGCTTTGAAAGG
446739 GATGAACATT
Statistics
Matches: 1013, Mismatches: 81, Indels: 45
0.89 0.07 0.04
Matches are distributed among these distances:
27 10 0.01
28 431 0.43
29 495 0.49
30 52 0.05
31 22 0.02
32 2 0.00
33 1 0.00
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (29 bp):
TGCCACTGACTTGTGGGCTTTGAAAGGAG
Found at i:447971 original size:1 final size:1
Alignment explanation
Indices: 447967--448018 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
447957 TTTTTTGCTA
* * * * * *
447967 TTTTTTCTTTTTTTTTGTTTTTTGTTTTGTTTTTTTTTGTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
448019 GGGTGTAAAG
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (1 bp):
T
Found at i:447981 original size:10 final size:10
Alignment explanation
Indices: 447957--448015 Score: 64
Period size: 10 Copynumber: 5.6 Consensus size: 10
447947 GACCCTTCTA
* *
447957 TTTTTTGCTA
1 TTTTTTGTTT
*
447967 TTTTTTCTTT
1 TTTTTTGTTT
447977 TTTTTTGTTTT
1 TTTTTTG-TTT
447988 TTGTTTTGTTT
1 TT-TTTTGTTT
447999 TTTTTTGTTT
1 TTTTTTGTTT
448009 TGTTTTT
1 T-TTTTT
448016 TTTGGGTGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
10 22 0.52
11 15 0.36
12 5 0.12
ACGTcount: A:0.02, C:0.03, G:0.10, T:0.85
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:447988 original size:27 final size:27
Alignment explanation
Indices: 447957--448016 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
447947 GACCCTTCTA
447957 TTTTTTGCTATTT-TTTCTTTTT-TTTTG
1 TTTTTTG-T-TTTGTTTCTTTTTGTTTTG
*
447984 TTTTTTGTTTTGTTTTTTTTTGTTTTG
1 TTTTTTGTTTTGTTTCTTTTTGTTTTG
448011 TTTTTT
1 TTTTTT
448017 TTGGGTGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 3 0.10
26 9 0.30
27 18 0.60
ACGTcount: A:0.02, C:0.03, G:0.10, T:0.85
Consensus pattern (27 bp):
TTTTTTGTTTTGTTTCTTTTTGTTTTG
Found at i:447999 original size:20 final size:19
Alignment explanation
Indices: 447974--448018 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
447964 CTATTTTTTC
*
447974 TTTTTTTTTGTT-TTTTGT
1 TTTTTTTTTTTTGTTTTGT
447992 TTTGTTTTTTTTTGTTTTGT
1 TTT-TTTTTTTTTGTTTTGT
448012 TTTTTTT
1 TTTTTTT
448019 GGGTGTAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 3 0.12
19 12 0.50
20 9 0.38
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (19 bp):
TTTTTTTTTTTTGTTTTGT
Found at i:448016 original size:22 final size:21
Alignment explanation
Indices: 447967--448016 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
447957 TTTTTTGCTA
447967 TTTTTTCTTTTTTTTTGTTTT
1 TTTTTTCTTTTTTTTTGTTTT
*
447988 TTGTTTTGTTTTTTTTTGTTTT
1 TT-TTTTCTTTTTTTTTGTTTT
448010 GTTTTTT
1 -TTTTTT
448017 TTGGGTGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 2 0.08
22 22 0.85
23 2 0.08
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (21 bp):
TTTTTTCTTTTTTTTTGTTTT
Found at i:448019 original size:14 final size:15
Alignment explanation
Indices: 447967--448018 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
447957 TTTTTTGCTA
447967 TTTTTTCTTT-TTTT-
1 TTTTTT-TTTGTTTTG
*
447981 TTGTTTTTTGTTTTG
1 TTTTTTTTTGTTTTG
447996 TTTTTTTTTGTTTTG
1 TTTTTTTTTGTTTTG
448011 TTTTTTTT
1 TTTTTTTT
448019 GGGTGTAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
13 3 0.09
14 9 0.26
15 22 0.65
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (15 bp):
TTTTTTTTTGTTTTG
Found at i:461098 original size:22 final size:22
Alignment explanation
Indices: 461070--461124 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
461060 TGGACATGTT
461070 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
461092 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
461114 AAAAATGCATG
1 AAAAATGCATG
461125 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:462085 original size:20 final size:20
Alignment explanation
Indices: 462038--462112 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
462028 AAAAAGACAT
*
462038 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
462057 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
462078 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
462098 AATGTATCGATACAT
1 AATGTATCGATACAT
462113 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:462106 original size:40 final size:39
Alignment explanation
Indices: 462035--462112 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
462025 GGTAAAAAGA
* *
462035 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
462074 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
462113 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:462425 original size:60 final size:60
Alignment explanation
Indices: 462359--462546 Score: 215
Period size: 60 Copynumber: 3.1 Consensus size: 60
462349 AAGTCTACAA
*
462359 AATGACTTGGGCAAAACCAAGACTCAATGAAATGGCCTGGACGAAACTAGAAACCTAAAC
1 AATGACTTGGGCAAAACCAAGACTCAATGAAATGGCCTGGAAGAAACTAGAAACCTAAAC
* * ** *
462419 AATGACTTGGTG--AAACTAAGACTCAACGAAGATAACCTGGATA-AAACTAGAAACCTTAAC
1 AATGACTTGG-GCAAAACCAAGACTCAATGAA-ATGGCCTGGA-AGAAACTAGAAACCTAAAC
* * *
462479 AATGACTTAGGCAAAACCAAGACTCAATGAAATGGCCT--AAGTAAAACCAAAAACCTAAAC
1 AATGACTTGGGCAAAACCAAGACTCAATGAAATGGCCTGGAAG--AAACTAGAAACCTAAAC
462539 AATGACTT
1 AATGACTT
462547 ACGTGAAACT
Statistics
Matches: 106, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
57 1 0.01
58 1 0.01
59 17 0.16
60 70 0.66
61 17 0.16
ACGTcount: A:0.46, C:0.20, G:0.16, T:0.18
Consensus pattern (60 bp):
AATGACTTGGGCAAAACCAAGACTCAATGAAATGGCCTGGAAGAAACTAGAAACCTAAAC
Done.